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If a run-time error is generated, add the menu item. H!J NlWorksheet Menu Bar B%D!F%L. &SNP9Pq` Rl !F%L."X Set convertHapmart072HAPLOVIEW = objCmdBrPp.Controls.Add(Type:=msoControlButton) Rl !F%L.0M Set transposeSNPHAP = objCmdBrPp.Controls.Add(Type:=msoControlButton)LH Set CompareHAP = objCmdBrPp.Controls.Add(Type:=msoControlButton)$ CompareSTR.BeginGroup = True%LA Set sep = objCmdBrPp.Controls.Add(Type:=msoControlButton), LOHstretch.Caption = "Find &LOH stretch"%L% Hotspot.Caption = "Find &Hotspot"LA@Vk Disables the error handler.BrPp =& Set properties for the new menu item.ols.About SNP tools "(P, shareStretch.Caption = "Common &Stretch" ((Convert to H&aploview and Plink 0(P2 transposeSNPHAP.Caption = "&Transpose S&NPHAP"/ convert2Phase.Caption = "&Convert to Phase". CompareHAP.Caption = "Co&mpare Haplotypes"e 2 CompareSTR.Caption = "Sharing N of STR allele" sep.Caption = "-"J convertHapmart072HAPLOVIEW.Caption = "Convert Hapmart0.7 to Haploview"& LOHstretch.OnAction = "LOHstretch" showAbout "(X= convertHapMap2HAPLOVIEW.OnAction = "ConvHapMap2HAPLOVIEW"*(Conv2HAPLOVIEW 0(X+ convert2SNPHAP.OnAction = "Conv2SNPHAP"APLOVI/ convert2PedPhase.OnAction = "Conv2PedPhase"NP) convert2Phase.OnAction = "Conv2Phase"& CompareSTR.OnAction = "CompareSTR"AP  sep.OnAction = ""removeOldButtono@, This procedure deletes an item on the Tools menu on the worksheet menu bar.* If the Project command exists, delete it.SNPWorksheet Menu Bar B%D%FB@\oH Set LOHstretch = objCmdBrPp.Controls.Add(Type:=msoControlButton)E Set Hotspot = objCmdBrPp.Controls.Add(Type:=msoControlButton)J Set shareStretch = objCmdBrPp.Controls.Add(Type:=msoControlButton)U Set convertHapMap2HAPLOVIEW = objCmdBrPp.Controls.Add(Type:=msoControlButton)L Set convert2SNPHAP = objCmdBrPp.Controls.Add(Type:=msoControlButton)N Set convert2PedPhase = objCmdBrPp.Controls.Add(Type:=msoControlButton)K Set convert2Phase = objCmdBrPp.Controls.Add(Type:=msoControlButton)O Set OR_MantelHaenszel = objCmdBrPp.Controls.Add(Type:=msoControlButton)H Set CompareSTR = objCmdBrPp.Controls.Add(Type:=msoControlButton)O Set transposeTextFile = objCmdBrPp.Controls.Add(Type:=msoControlButton)C convertHapMap2HAPLOVIEW.Caption = "Convert HapMap to Haploview"2 convert2SNPHAP.Caption = "&Convert to S&NPHAP"6 convert2PedPhase.Caption = "&Convert to &PedPhase"6 OR_MantelHaenszel.Caption = "OR (Mantel Haenszel)"> transposeTextFile.Caption = "Transpose external text file"$ Hotspot.OnAction = "FindHotspot"+ shareStretch.OnAction = "CommonStretch"B convertHapmart072HAPLOVIEW.OnAction = "ConvHapMap072HAPLOVIEW"6 transposeSNPHAP.OnAction  5 ) O!k6#oFdI"FP(kiDbBxME[LSS< < $<8<<<<< <$<(<,<0<4<N0{00020819-0000-0000-C000-000000000046}p @`DDee X % "x% &) T% (o th% *orks% ,@, 20% .% 08% 2X% 4x% 6% 8% :% <% >eo% @`8on% Z`D g  %@i%e%p @@@@@ @``hNRV@ @ @ ( @ @ 8 @ `x @h @X @H DX`% @ @ (@ ( @ @   @`~Pr " 0 &@ >h * 2 (08@HPX`h &p  *  * @4r` ,  ( 00@@   V N L PX V  ^ \ R T@ T` R N H V Nh * V   "  ,8 2` , 2X, J 8` 8 < 6 40 <  8h D P @ , *` 2 DX H 2 < 6 00 ,P   ,` . 6   " 2 & 08 h 4vp  x) This procedure adds an item to the Tools menu on the worksheet menu bar.8Aug 24, 2007 add frmTransposeTextFile, Bowang Chen, DKFZ$ This will be set to the Tools menu.]@+ This will be set to the Project menu item.]`]]]]]] ]@]`]] Dim sep As CommandBarButton]]]] @# This generates a run-time error if the menu item is absent.$ Create an object variable re= "TransposeSNPHAPoutput"& CompareHAP.OnAction = "CompareHAP"( OR_MantelHaenszel.OnAction = "OR_MH"0 transposeTextFile.OnAction = "transposeText"xAttribute VB_Name = "ThisWorkbook" Bas0{00020819-0C$0046} z@GlobalSpacFalse bCreatablPredeHclaIdTru @ExposeTemplateDeriv#@ustomizB0Option -licit P $ Sub _AddinInstall() '  procedure adds an item to the Toolsmenu 1 wsheet bar. 'Aug 24, 2007$ fr@mTranswTextFile, Bowang Chen, DK`FZ Ewill be s- @.B Dim objCmdBrPp As CommandBa@rPopupProjec.A: AboutKButtonLOHstretch Hot=shS convert2SNPHAP=t[ LO0VIEWZD Ha pMap2 2PedPhAjLV#_ =p@'`2'I9DseC,STR:OR_MantelHaenszel&0%^*@mart07+ BQO@}rror ResuNkhgenery run-tie"ifyw}i@bsental' @nmevariBref@ ing tS@xAt= Appa.`/Dvs("MÉMx") n$tr@("`Y")Cd a c~ inBfourth i Dda' If@"s e&d, $C#Err.Number <> 0eCAOB.@( _b aType:=msxoCo#C#Wi G.J.CaC &!*End !#=2-CkA`? e2 To" p#o(*Wc JPJAV@ [ooomeik grlgl!n///&m auW.BeginGroup3wook"@showOP!RIusDis-apsa3uhЧle@qyGoTo 0B'CжpМ`ies f|QxnewjrCfB9[ [p "VFi ]& TTdYR m@u&4"B ~PH&aplo vi Pli>nۂ$t 3D up5&rQS&24ele48external t| fP@%pHAPLOVIEW.Caption = "Convert Hapmart0.7 to4loview" About.OnAcvshow*" 'LLOHstre8tch L,'Hotspo KFind%shareSOCommonc2H /{Map 7 0!2SNP\YC transeT put 2PedPhaseE T  @bvpi/mBgsepSTR & OR_MantelHaenszel AHD JTextFilK=2 on the same chromosomeusage:1. run the macro LOHstretch()X2. select the data area includeing 5 columns: SNP_ID, Ch, Loction, call(genotype)and LOH&3. tell the macro where to put result. 4. click RUNBowang Chen, DKFZ, 16.03.2005]x]]  z B@ ~ B@ SNP ID55 5, Chromosome55 5,Location55 5,Distance55 5,qx''  !  ! A@h! read a SNP into SNP(3) temporary &6F5  5 5%5  5 5%5  5 5%5  5 5%5  5 5%$B@q0$! new LOH>=2 SNP found$$B@$$B@'d$$%$$%Lsame LOH and same chromosome$$B@  'd9different LOH or chromosome, then output previous stretch  G$$  A@j$$B@$$B@'k@k8k0   G$$  A@j 5B@H555%5   5 5%5%B@H B@qpoh@  !5  5 5, !5  5 5, !5  5 5, ! ! 5  5 5,  ' !5  5 5, !5  5 5, !5  5 5, ! ! 5  5 5,  'qoxAttribute VB_Name = "frmLOHstretch" Bas0{B1DBF724-F6B3B-1-92A6DD27973F43}{891E92FB-ABF4-E442-8383-F7CB65EA66D3} cGlobaBlSpacnFalse Cre atablPr@edeclaI"dTru @Ex0pose .TemplateDerivCustomizBOption .lichit P!% Sub UserForm_Initialize(() Orror Resu@Next ' M0e.Ca+SNP tools: "Image1.Visi setStatu@sBar 0 With Percent.Top@IprogresA ALeftHeighG Wid="M-End MA) M IPCommandButton1_CYkPBJ2.EnOf"?Me%MousePoinHter8fm HourGlass! FindG Sce:=RefEdit1, TargetF2dDefaulGdPnLHid/NI'VI2XI1$)ce'%3I)(L S As Single\pDim `nrg$IfeRA@D Then 'clfe W= iff)PU^a$aAN(0 aP2%yhF* )+8RoundM* 10.) & "%?c(?k"If DoEvsG'This m@acro fs0 theaZ w >=2 Bchromosome 'us\: '1. run 'A2. @select"d a@acludej 5 co0lumn_ID, Ch, Loc, call(genotype)h@ '3@. tell(wheree pu t 0`H. '4. cV RUN 'Bowangen, DKFZ, 16.03.2005zZR(RW?R&A (3)New /1 !iqLong, jkc1FrcSHqInfo, tBZct2s.\Shee_IK3`BB/R .Q.C@s(.row{r0t, . +( 0)i" I^D-1Co'2%a?%`0Distance6k 3Vj1 iq To wNo - C AJi / (1 s%'-ad a!%@4to&toraryufQ`0.D9odim, _50$t22)mt= 3w    4z"@ 90A >= 2߂J`R%$n0DsX fbNq1:)EFZ!NP(23w A*QvuW Equ alCH(2)Ph3).P c 'sep ]xf ;! k'n 'diffpcnt 1@Voutepreviouser> 0߃p1p&# K\`/0; qQ+7ԃ/ A iutBQ;2qinof83o7 .srcSheet.Range(xCells(.rowStart, .col(), L + j0 - 2\$3)).Select ion.CopyEnd@ With Sub Private outputLOHstretch(Snp1 As SNP, snp2c getfsInfo, B0yRef>Long)?=  Wvt0) = M.>NPid"1"CH1!2 !Loc!3U3v6Ijz       >N ( 8>NH   P  ` p  x    @  B       *(   @  X  h  x             B   >z  8  H btP        >J  &,0 X   ` h p x B Uljx6My)-kfxR R ME "@0L""> <<<< <$<(<,<0<4<8<<<@   ` `+$ `@ i(+&h `@  ?)0   ` ` ( `@ . `@ 2( `@ 6h `@ & `@ : `@ B( `@ Dh `@ V `@ Z `@ 8(`@  :h`  ``@ d`@+hH`@( ij+r`Dijit+v( `@ .i+z!`h!Di~+"`x@"Ti+H#`@(# pi+$`$ yi~+%`@% i+h&`@H& i+'`@' i+((`@(i+)`@h)ii+(*`@*ii++`@h +)%) %````+p,`@X,i @ %```` H0P +(-`@-i @ %`+.`@h.#i % @ %```` h +/`@/((2i 8@  %`xg```+0`0Zi 1`$@01BBniPi %```  @( x`+2`2)%ii (i``(H( h ( ( h(  ( X h (8H p X 0 Hh@h !xhh!h !@!( ! +3`@3i8iXi xi+4`4i~i r`@(H( h ( ( h(  ( X h (8H p X 0 Hh@h (' ^e(H( h ( ( h(  ( X h (8H p X 0 Hh@h (H( h ( ( h(  ( X h (8H p X 0 Hh@h (H( h ( ( h(  ( X h (8H p X 0 Hh@h (H( h ( ( h(  ( X h (8H p X 0 Hh@h 8nF '( @ @ ' @| p0(l @\ (((p0( ((p0 p0 x)x)))p08 ) (p0@p0 * @ X*( @ @ * x*@| p0(l @\ X+p0++`-,,H,(,p0h 8,p00 p0 p0 p0(0-0-h-H-p0H X-@p0 . .X.8.p0HH. .(.Xz|@.@ . @ p0 @ X@ @p0X p0@ @ @ 0h0(08n>880`0p0 8n= 0( 0@ @  n( @p @l 111 n8 12(2 2@2hP2 22X  n( @ @ X2 n? 2 2 3`333 nX3444 @4 04@ 4( @ @ n( @x @t (4 np  x5X555 n5 n n (6@ X6 @  n( @ X8x(7`7@7 nP7 n n @ 7 @ n( @ 8888 n(8 n@ n @ X9 @ n( @ (: (:H;@: nh P:x: : :: ; ;X `;( @ @ 8;H;? x; n(`; n ;0 8< 8<X=P< nh `<<< << =0=X p=( @ h@ H=X=? = n(= n = (@ ( H>h?`> nh (p>>> >> 0?@?X ?( @ @ X?h?? ? n( n ?P X@8 X@xAp@ nh @@@ @@ @APAX A( @ @ hAxA? 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B  ! B! $! $ " $H" $p" "":h":h"8#@# VH#B  # # # 4# R$h$ &p$$$ $ $$R$%0%88% JX% Jp% %&  & (&B8&X&`& B  h& Zp& N& '('H' FP' h'x',''*' ' .Z'((Z0( (( ( .((( ((B  ) Z) Nh))))) ) .Z*0*Z8* ** * .*** *+ B  +++8+ F@+ X+h+,x++*+ +++ B  +,,  , ,0,`,2h,, , .Z,,Z,  @- *H-`-h- p-$--- @- (- 4. H. "P. ,x. . ,. $./ / ./ / 0 *0 H0 X0 B  p0 &x0 00&0 00 &0 0 1&1 101 81@1H1P1 "  X1 :`111111 12 282P2h22222223(3@3X3p3333334404H4`4x4444 ,4&505 &^H5&^p55&f5 5  56 :|6 4vX6 66X6 7 7 (7  87 B  @7H7 X7 `7&h77 (8 88@8 H8 X8`8h8 B  p8 "2x88 8B  88 8:88 9 09H9 X9h9 $p9999 9xsome SNP functions, such as:to infer haplotype of offspring by the genotypes of trios,.to compare genotypes or haplotypes of smaples,<to compare homozygosity, heterozygosity or NoCall in samples#Bowang Chen, July-August 2004, DKFZ]0 ^8^P^hp   *SNP Tools 1.70 is successffully installed. <http://www.dkfz.de/de/molgen_epidemiology/tools/SNPtool.html 7http://www.bioinformatics.org/snp-tools-excel/index.htm ,Bowang Chen, DKFZ, Sep.21,2004 - Dec.07,2011  SNP ToolsA@op 1KTA'2KTB'S 'ni ]]' $  $! !d? !d'  'dP   'k0d('k k  TRUEFALSE$'iAPublic Function CompHAP(Hap1 As String, Hap2 As String) As String$ If Hap1 = "?" Or Hap2 = "?" Then CompHAP = "" Exit Function End If If Hap1 = Hap2 Then CompHAP = "TRUE" Else CompHAP = "FALSE" End If End Function](  %  %  % ' AABBAAKAABBBBKBBAAAAKBBAABBKAAAABBKAAAAABKBBBBAAKBBBBABKAAABBBKBBABAAKABAABBKABBBAAKNoBBAAKAANoBBKBBNoAAKNoAABBKNoBBAAKT!'!'AAAAAAKNoAAAAKNoNoAAKAANoAAKAAABAAKNoABAAKABABAAKABNoAAKABAAAAKABNoAAKT, "BBBBAA", "NoBBAA", "AABBAA"A'A'AAABABKAANoABKAABBABKABBBABKNoBBABKTA'B'BBAAABKBBABABKBBNoABKABAAABKNoAAABKTB'A'BBBBBBKNoBBBBKNoNoBBKBBNoBBKBBABBBKNoABBBKABABBBKABNoBBKABBBBBKABNoBBKAAAABBKAABBBBKNoAABBKTB'B'S?'?'n` G'j   $'i @]]AA' $  $! !d?AAABBB !d'ring  'dx   'kXkP Gyj8  i ]  %  %  % '  NoAABBKAABBBBKAABBAAKNoBBAAKBBBBABKAAAAABKAAAABBKBBBBAAKT1'S0'n d BBBBABKAAAAABKAAAABBKAABBBBKBBBBAAKT G1'cG'jS'nki    1$' i@    1$'i    1$'iX]] ' $  $! !d$ !d'  'd   'kk Gyj i8  %AB$'i] 0 '  $  $!  !d$'  Gj iH  %NOCALL$'i ]( @ '" $  $! " !d$'" "Gj( iX AA BB $'$d'$ki ]8 P '& $  $! & !d$$'& &Gj0 ih *B@,o 0B@,o 4B@,o( 8B@,oh `B@,op  <5>(@C@,q@o8 B@,o( .. 5F(f5H(f5J(f5L(f5|(f5N(@5P(f5R(f5T(fC@,qP oH h XB@,o(  \B@,o  ^B@,o ( frmSTRshared.Showo h bB@,o  fB@,ox lh 8 get the attributes and ensure that it isn't a directory j$n p'hl 0 if an error occurs, this function returns Falsei H tG.'tj j'r j j t %'riX KThe following 2 function convert SNP A, C, G, T into 1, 2,3,4 respectively."for the input format of HAPLOVIEW.missing value will be 0.Bowang Chen, DKFZ, 20042this returns code for nucleotide style: A, T, G, C  %x' KT $z 0'vKKKKT  %$z   %|$z'v Case 3& Select Case VBA.UCase(SNP) Case "HET") SNP_ACGT_Code = "3 0"! Case "HOM", "DEL") SNP_ACGT_Code = "0 0" Case Else) SNP_ACGT_Code = "0 0" End SelectS@0 0'vn(i (2this returns code for nucleotide style: A, T, G, C ~AKaKT'zCKcKBKbKT > B and b are set for those data like in SAS haplotype example1'zGKgKT'zTKtKT'zS'znithis is for SNPHAP,>this returns insert blank between nucleotide style: A, T, G, Cmissing data become "0 0"  %x' KTACGT   0'd0 0'kKT  %   %|'KT  %HETKTG 0'HOMKDELKT0 0'S@0 0'n(S 0 0'ni:this returns code for genotype style: AA, AB, BB or NoCall KT  %$   %|$'S`0 0'nHi@H<this returns code for nucleotide style: AA, AB, BB or NoCall ~AKaKT'BKbKT'S'ni  %GGKT'TTKT'S8'n(i   %GGKT'AAKT'S'nih  %AAKT'CCKT'Sh'nXiP  % 0==AA, 1==AB, 2==BB, -1==NCK0KTAA'1 1'K1KT"AB"1 2'K2KT #"BB"2 2'S"NC"0 0'nXiP(?Bowang June 27, 2007, for BC 900 case-control copy number study  %KK '* Kora samples are all controldC '* others are casekpih Sub test1()E Dim nSample As Long, i As Long, n1 As Long, n2 As Long, k As Long& Dim str1 As String, str2 As String nSample = 12 For i = 1 To nSample str1 = str1 & "0" str2 = str2 & "1" Next i n1 = BinaryToDecimal(str1) n2 = BinaryToDecimal(str2) For i = n1 To n2 k = i1 Debug.Print DecimalToBinary(k, Len(str1)) Next iEnd Sub<return the number of a SNP genotype of specific neucleotide,SNP_N_of_neucleo("TT", "C")=2SNP_N_of_neucleo("TC", "T")=1SNP_N_of_neucleo("CC", "T")=0SNP_N_of_neucleo("CC", "C")=2' Gj   % G  'j   %| G  'jiPPublic Function GenoConcordRate(Sample1 As String, Sample2 As String) As Variant( Bowang /DKFZ Dec 07,2007.to compare genotypes in 2 lines, many columns.Kgenotype in every cell, format like "A G", "C T" or "0 0" (nocall, missing)] Dim S1 As Range, S2 As Range]] S1 = Range(Sample1) S2 = Range(Sample2)' !! !! Diff. Long'd  !!  %'  %' 0 0 0 0    %  %|  %  %|  'k   !!d'kiS this function will return all genes with distanc < 10K, including CDS, UTR, etc...G Dim myAnno As New Affy_annotaion 'why this does not class now work?]x]] ///$' ' h  UBound(geneStrings) 2 $ $B@  $!  $!Gjk  $!$' $!--- $!   ///'k@  $!'k  ipS this function will return all genes with distanc < 10K, including CDS, UTR, etc...G Dim myAnno As New Affy_annotaion 'why this does not class now work?]] $'    $!  $!Gjk  $!$' $!--- $!   ///'k8  $!'k i(]] 8]P ///$' '   UBound(geneStrings) 2 $ $B@  'i]]H`x $'& If UBound(Genes) = 0 Then GoTo out'$!$'    $!  $!Gjk   $!$  $!--- $!  ' $!'k  $!'`iX9Public Function closestAffyGene(Anno As String) As String! Dim Genes() As Affy_anno_gene. Dim i As Long, j As Long, distance As Long Genes = AffyGenes(Anno)& If UBound(Genes) = 0 Then GoTo out j = 0% distance = Val(Genes(0).distance) For i = 1 To UBound(Genes) If Val(Genes(i).distance) <= distance' And Genes(i).gene_name <> "---"' And Len(Genes(i).gene_name) > 0 Then j = i( distance = Genes(i).distance End If Next i$ closestAffyGene = Genes(j).briefout: End Function CDS CDS'dX UTR UTR'd( exon exon'd intron intron'kkkki4 Usage: arrange_MALDI_TOF "","" in immediate window]p]]]]H2456+891037+N3579+N46812+ rs10454452+ rs11236365+ rs11581382+ rs11641748+ rs11897813+ rs10817960+ rs12296076+ rs13069836+ rs13095210 + rs1469808 +rs160236 + rs16823149 + rs2885984 + rs2936190+ rs3903983+rs396577+rs4560+ rs4743193+rs533233+rs646900+ rs6495026+ rs6505339+ rs6561324+ rs7115764+ rs7178409+ rs7868550+ rs9582219+ GCo_Ca_all!A2:I32904'j G out!A1:I32904'j   B@Plate  !,Smaple  !,   $  !,     $      !,       !,  A@  $  $$      !,   o]H`'  5 ) 5   5 5% 5   5 5% 5   5 5% 5   5 5%'k qi  $  $' G--'jix=] ' ~X ~x ~0       ~' d< ~ '+expected dosagek<k<i<HFAttribute VB_Name = "SNP_functio n" Op Explicit `' 'so s, such as 'to infer haplotype offspring by the gen8sos,;com8par J-smYe /homozygosity,@ heter or NoCall sample 'BowaIChen, July-August 2004, DKFZ Dim transxHAP As frm Tpu IDShng HapLoci ProBb End & Sub showAbout()"MsgBox Tools 1@.70 iscessffullyostsed." & vbCr4Lf_"Q"http://www.dkfz.dDe/mol@d_epidemio@logy/t/@:.htmlbioormatics.org /snp--excel/ind "?" T@}*=$`0A9dAA .j9eD * ( ae$AberrqpTorqal SexQ$q !'enf%Uoopo`07`D7q_qob1N2F"MAAB", " AANoBBHABtA$BLtA" Aberr = "1.Case 0ElseR(End Select) 2 KFamGenoN"SIfA@'M'ZO'M';O/'@d'xGConcord(ParamArray myRanges(oVariantBoolean#Dim cxObj, iaLong0Ag1 Q`TrutFMiao UBound()B~Each`InGi).Cellsa`lNot IsNoCall(c.Tex n c= ` !0@""BvNa .NA"* (f '!ez{Pd!I Exit *fN@$ i out:rJIsHetero"=NH`(VBA.U!)!+BaB, FaD%_ZA_ZFZ UhUqU *X#X5=;k;GoTo @8; ;hG;`%;NOCALL^?i3OKKK FO= IROIIAO D;O O><_9om3<8[O<4f a 1" |OrW)RcZQ?b+LaF H /"/"/"/"*"i hkt"""@cCl=?G2 ?]]Sub Common| etch( frmj.Showa;nv2HAPLOVIEWHaplovi50.Ope7osj2S .RefEditadResult?Cnvert_D.Win/gb6 ܅/2PedP~h  Sv2M1mpare '-p9?:"eSTR() '" frmshared.Show End Sub Public( OR_MHOR R TtransposeTextdT ,FileAFunction "Exists(f-Name As String) Boo lean On Error GoTo Handler' get the at@butes  ensure at isn't a dire`ctoryE = (GetA"GJEvbD)Y0 GA:Bif: eToccurs,=is fzreturns FalseParse Mn, Opal DELIMITERS'PResuZNo If= "" Then." J$AmVBA .LeftF., In$-) - 1)C ' '" follow 2Qconvert SNP A, C, G, T into 1, 2,3,@4 respyively. 'finputrmof HAPLOVIEWmissvalue will be 0@ 'Bowang CG@, DKFZ004 Nn%_ACGT_Code(ǂ( e'thEc % nucleotide style:8T8&CBZ= WTrim)el@; Case Lenh1a9All +) & " 0?2, 3, 4, 5 e fB@, > "` nARightbmf3aSaU?C aeb"H8ET"k #"3! OM", "`Y @: l0 E nº 2" ew !HAfN\5Integ?@?]4]: +"AA/aSaN [^UC?CcBb " ' Bb 9 sɣ data like SAS haplotype examplejU2Gg3Tt4 0"zN(6?gT #oPW@V,DOins!\ blankPVtwepgO]O'Y"becol"0`?QctQ1S  qj"Q\0) > 0q@& SQ?Ah' 1Ifb+G$v0R"QUJT %6T9S4T "GNMSi6b$.U_PoRBvgenCFQ0AB, BB 5NoCalloр#AC +@T $/z z1Q`'/CGɽ gg &EAOO3g0݃_wE2"fqN[O)E)G%_թlו{0%`)q#GGi T@5 >ߣ%%!A90# qGQ"AA_nG eZ$A 2 End Select PFunction Public < Geno_AC_Code(0type As String)Integer Case `VBA.Up)F "AA"C m = 0 .C C.1 .Else]brlmm2AB(c6) 'B0==AA, 1B, 2==Be-NCV0, "0" 'AcADBb'Bowang Ju ne 27[00@for BC 900 c-c@ontrol n study ]IfLeft F"o)_K" Theng .D& +' Kora s4s are a>l ʭOC" Lother'3If'Sub test1(cQ Dim n+ `zLong, iGn1h2gkEBZstr/,(rE @= 12 'cF1i %1 Toe#] = 1aJ2 2Aak Next i= BinaryToDecimal(A n2e`aak  DebuHg.P t To (k, LeNn e 'Bbub N`SNP_N_of_neucleop,`b1,`8 'ret0urn @CEZof a g`¸i sp"f tide, '"TT"C")V= CT1@0 W -q)Ep0p Go4out> 0 Abby%dyN,C yN+ 0 a$ R0ightf7_ eoR :y 'ConcordRateĕr}9"#Variant^(1 R0Ue, SRJUW/DKPFZ '0 PW2!W 'toPmpaOU(s in 2 lines, many lum`ns. '*0everell," \mat@ke "A G) T" D"g (nocUissb!OMCB!S r 62s6,rXϰdQ= %@ GDU%0& S1.CocCount <><h%"Diff. By)Xg 1= As:(Pi%US2.C/ @ #Ord=@ 1 2_ hen # 'i).?_name& - 1 T Go4skip_repeat(End If:ValE&(/e)00h0 _AD<> "---"Len+[) 8 brief[l>2 D B & "///". L>;X:Next i FD Publ8ic  St[Ő(ÇG,D jE, NsVarianfs3ZSplit(A,XC(Nĵ iRe/NCaN 'U4Set i) zq!.setZuse [d4AM +7A7closestEB!*&b8((';!*7eq be)c@z)a&ojuc?j`0 =b g0).K61_ AB !(a``0_e_ ` K=eߘߘTa*i h+ eNU(j).#::W'?W $W'A[WFWbW'S + +l+?b+ +nce41F+c $pz$rpy$q$$*$$N$C$'"$'FkOpPexon(AssocAOQQ ".In%cp"_4a"A"ElseAP <z Q` PQA ^A_ intron74 yg ,aFSub arrange_MALDI_TOF(sourceArea, targ et[A8Usage:o "","" imme diatendow QHmy#`hdInfoFHng, k SsPl(@4Azm SNP27ample38qw"2456SS0= "89103 7y3N3579iN46812s rs104544512363657581388364174 875u1897 P68179<600 22-p7Q 8530P698399H521104%00 1160 16682314rE28805984HE2903619E3903` 8E39657b54743193A533232U6026495022X65026561322711576717840786855 9582210R1BIf< sourceArea = "" Then Co_Ca_all!A2:I32904" If target | (@out!A1 pmyStretch(es.>s Infoz,\n :rstSheet.Cells(1, i + 1)Plate22SmaplFor&= 1 To UBound(SNP)A}$*(iNext i 3jW/3]4k384AC(j -Y* k,s1(j2Mk{ $A+i 4 NADoEventsJXV4A}"loo kfor(, :, k, c=f5jB(End Sub Priv Function  As ran"frmSNPHAP: ;wcGI &0lxME (SS S<N0{FCFB3D2A-A0FA-1068-A738-08002B3371B5}8b<@bD@,!h i  Ah i `8%b4@b8@b(@ @(xh % ((xh(xh(xhPhH @ x` ` @` ( ` @ (` X ((J  xh8(8P ~P  ( *0 `  B "  x]@h]@]@]@]@($Property Set SNP(newSNPid As String) SNPid = newSNPid End Propertyx 'mP 'm80x|Attribute VB_Name = "ABCD" Basd0{FCFB3D2A-A0FA-1068-A738-08002B3@371B5} zG lobalSpacFalse CreatablPredecdlaIdAE xposeTemplateDeriv$Customiz COption .licit P!% SNPID AHs Sng C"h Loc Lo omp Boolean Geno + 'Property SeBt;(new>id) ' =  'End ^ Pubd  GID()Variant A6=8  LByVal vNewue>)@&FrU~|   "  "$ "(  H  Xh 0p 0 0  " d   "   4(` $D$DB(B8 *RH,Lx F F F F  6( `h : :    (  @X `(hx@ .`  8  H  X  ` 4p   &xj*&2LLk>IOPKti>p񜖯țM_)oEv$dJ .6D\6x`@`B D8 @% Fx`  R`8@)8 (%)THPA%iF `` W%`X``Z( L `@H 66iFh)8%)T A% d@%`fh ```h`@`B`:`jP`l ,l ``@  ip i  `x p H % x  % @@  %^H  %P X 0 @@ @@ @@!   ` P ` p|h` X @    ( (phjn X @  @ AH `` |h @ @ h @  h@ 8hPh0.h @ @  ( @ @ @ (`Xh  (p @` \  X 8HT `pP L !H ! (8 @( &`()$ `(xj@80  `hX(hP`h0 (` ( @ H@ (  H@ HH0`@(@(@ @ @ LP  (JLP  8H X @ @  % @| l P@\ HL @< P, pP( `8X @ @ @  @Xb `@ @ ` @  X @t @d `  \  X P`(V @P xL (H @8 8H hxR`H  `  0( @ H X  x  (@ @ | (@l \ @L `(< @, @ ( @ @  @    )0  p!!!  !8!H! `!p! !!X !@ @ ! 8"@ @ @ !@ _ @p #,@` 4! H x  ~P   `h  ( b ` h " 8  "            (  0  0H  X  `  h  p x   "  "   8  N        B ( 00 ` p x      & &  ( H (` x           (  @ "H 6`     2<    <N @ H h  r 0 H  <`  & > :( h "    ,*" 8v 8P :   4" &b >v( "h<  8 :  ( 8@ " Hh x 8    & , LH     @ Zp     08H `h p   ( 0 8@B HP X`:fx  xPrivate Declare Function FindWindow Lib "user32" Alias' "FindWindowA" (ByVal lpClassName As String, ByVal' lpWindowName As String) As LongCPrivate Declare Function GetWindowLong Lib "user32" Alias' "GetWindowLongA" (ByVal hWnd As Long, ByVal nIndex' As Long) As LongPrivate Declare Function SetWindowLong Lib "user32" Alias' "SetWindowLongA" (ByVal hWnd As Long, ByVal nIndex' As Long, ByVal dwNewLong As Long) As LongPrivate Declare Function SendMessage Lib "user32" Alias' "SendMessageA" (ByVal hWnd As Long, ByVal wMsg As Long,' ByVal wParam As Integer, ByVal lParam As Long) As LongTPrivate Declare Function DrawMenuBar Lib "user32" (ByVal' hWnd As Long) As LongPrivate wHandle As Long v9t |zA@ 9tA@hC@qo@o !(PoSNP tools: compare haplotype (P d(fA@h j n!l9l n!9 n!p9p99fqo v9t |z ~A@ 9tA@hC@q(o @- Dim hapID() As String, hapData() As String]] 8]Ph]]     ?!"#$%&'()*+,-./0123456789:;<=>@ABCDEFGHIJKLMNOPQRSTUVWXYZ[\]^_`abcdefghijknpqrstuvwxyz{|}~m]h z z! %'* ~ ~! %', *$.. ,$.. z$!0!'%蝄____  z$! '"(蝄___  z$!2'"____0 z$!4'%___0 ~$!2'$"____1 ~$!4'&%___10 ReDim hapID(0 To colNo), hapData(0 To colNo),   "`B@,      7 $ &  ,@      7 $  & ,.    "  "A@h  " '        7Gyj      7     7  ' kH ^B@,  $   &   ,.S 8 bB@,q B@H $ &$ $ " & " $$B@Hhe a Selection.Copyo ] clear and init (f  n9f9qX j$@9 n!p9p999fqd setStatusBar (0) n(f (ffollow j  n!9 A, C, d$%9P9fqpkhA@oX*Public Sub commonlength() ' As stretchInfo 28.09.2004](]H`xetur]de s] C]H' Dim Source As Stringz Dim myRange As New rangeInfoK z 8B@% On Error Resume Next| myRange 8!"':&  nSample = 5VB  : @0'@ B1'B  B$H'<e <D <F'>  <  <A@h_Code '  :$J +F $F 8 $DA@L $D!N > " $D!N'>End SeThe longest common stretch: > !(P(k  code The longest common stretch is: > PInfoA@i8 set back color =yellow With myRangeet .srcSheet.Selectpll range(Cells(.rowStart0, .colStart0), Cells(.rowStart0 + .rowNo - 1, .colStart0 + .colNo - 1)).Select* Selection.Interior.ColorIndex = 36 End Withblank 6mark the longest stretch of each comparison with colorecom For i = 1 To nComp setStatusBar i / (nComp)8 If stretch(i).Length >= Val(Me.MinLen.Text) Then4 markStretch myRange, stretch(i), haps(i)  End If Next i]p0 0]0 0 85B@H 5 T!\  'X  F retur5  F   %$ ' X $ X T!N  $$B@H% !^(` 0 0-test the other whether the hap is also commomode  F 5 F %$ 'ZK5  F   %$$b '  T!N x X  Z5% X  5%Gj8 ( X $ X T!N  $$B@H% !^(` 'qoaAs stretchInfoAAK]] 8P]hP F':  !h!d$'h, 'f 8 d(N 55   55%Gyj5   5 F %$ 5%!^!`%n`kXA@'l5   5 F %$ 5%'@  : @5   5   F  %$ 5%'l lGyj  l d!N d(N d!N  d(\k(d  d!N T!N d!\ T(\ d!N T(N  T(k d!N h 8 d FA@R'fk d(Nkxnp  f d!N T!N d!\ T(\ d!N T(N  T(k d!N h 8 d FA@Rk k q o ]0 'l  p p  % p   %'l lGyj i  xAttribute VB_Name = "frmCompHap"" Bas0{59DA10FC-F8B3-604D-8919-8F75DFAC9F88}{584BD4E9-0AAC-0741-A99F-5301ABB8D246} cGlobalSpacn False Cr@eatablPredeclaDIdTru @E`xpose.TemplateDerivCus tomizBOp tion .licit ' '&P"& DH FuncFindWow Lib "user32" Alias P_ ' "A" (ByVal lpClass!As Sng, lp/ ) LongNGetA ( (0hWnd&nIpndex7D"$S$ $E,dwNew@*ndMessageOSe )wMsgSx|@wParamI@nteger/l0YDrawMenuBarkOf)re +!B>LeftAHeighMWid@= 6 7U:1UeUaSh+Max U, Target&X2Gb?X".,,:k (c 1GSgc CaptionW ound(10\) & "%"O /DzIf DHoEvs Sub Private Func!commonLength(So6u@)etchInfo 'Public  ClC) ' 28.09.2004C$im myRanɀNew\ rpDiALong, j knSampInteger, nComp l@estU31S,2F=(@, hapsCB BQA('.getD# , " A On ErrtResume Next#c *%%=/.colNo / 2#*5F` i`T1 xTo $A 1` U0'U@2#2aX1# ic4= BinaryToDecimal(vRe(N( / E=Ō`Bb i I kc3 i)`$ToC(kNP@bpareHap#CqCEi),e/Mi i).Lj >  #Me.DHAP." x`:L&e AĊH9MsgBox  is , vbOKOnlyY=["eQ byellow#U\F.srcSheet.Spelec`%‹(C s(.row rt!`c 3 + a d- 1<, g3))].Irior.tIndex$36S  'mark the of each1W&iscwqorc;2/?&qI/?(P{>=L V9p$Mi!b.T`F)3A1q /$./d4W$%C4%iSub (!Zb5RR``?#Z7]6aEefmys#Work[B!Raic0BA){A1R !G)%Ptr! .) &]j@BMPB(A){*qcqp!.pj0 * 2pVB`A.Midv+y!.1)H Qyd3R, cF2RP[ J` q61Q5o1l17 j'tq|q1o@r wher@V`F o1momf2l c0@]t2 ue(j ; v?8 _ P;%L1i0 ) <> + #C< Go}ouɁ85qB!s(!!2Y!!0 >:vh!SB oYCwb.q:SDfoDpq8pER qA8temQ~2OGlaHstM\edBoonOHAH#V M nsJAlineConcor = Leng)/`xtH= 7b &Q@!Xe1"l ?v PG(jA) * 2jN>If Not A Ex8it ^ j  AtempStretch.LengthDq+ 11oӊBp@iE lsf > myÀ=4Info5ү$K E%I6N)P`A==CN PD@`= Min#amark>%Range, H, AlastMe2v)*&%0j $:fb[D@Ac<4$_Df_D_DhQ=-$T*!E+#_D _D_DRDD8iHAWith Sub Private Fun ctionh(mBy@T As ing)ABooleaDime0Long'= {i O )-, iA@ -* Fa`Bp Y!  % Add a command in the fourth positionwPar on the Tools menu.m As L" If a run-time error is generated, add the menu item.wMenuB H!J NlWorksheet Menu Bar B%D!F%L. &SNP9P!Prqh Rl !F%L." Rl !F%L.& Rl !F%L.(! Rl !F%L.* Rl !F%L.0 Rl !F%L.2 Rl !F%L., Rl !F%L.. Rl !F%L.4 Rl !F%L.6 Rl !F%L.8A Set sep = objCmdBrPp.Controls.Add(Type:=msoControlButton) Rl !F%L.< Rl !F%L.: :(T Rl !F%L.> showAboutk0 Disables the error handler.& Set properties for the new menu item.rkshAbout SNP tools "(P _Find &LOH stretch &(P Find &Hotspot ((PCommon &Stretch *(PConvert to H&aploview 0(PConvert HapMap to Haploview 2(P&Convert to S&NPHAP ,(P&Transpose S&NPHAP .(P&Convert to &PedPhase 4(P&Convert to Phase 6(PCo&mpare Haplotypes 8(POR (Mantel Haenszel) <(P sep.Caption = "-"Sharing N of STR allele :(PTranspose external text file >(P showAbout "(X LOHstretch &(X FindHotspot ((X CommonStretch *(XConv2HAPLOVIEW 0(XConvHapMap2HAPLOVIEW 2(X Conv2SNPHAP ,(XTransposeSNPHAPoutput .(X Conv2PedPhase 4(X Conv2Phase 6(X CompareHAP 8(X sep.OnAction = "" CompareSTR :(XOR_MH <(X transposeText >(XremoveOldButtono , This procedure deletes an item on the Toolsontrol menu on the worksheet menu bar.* If the Project command exists, delete it.`SNPWorksheet Menu Bar B%D%FB@\o x Attribute VB_Name = "DieseArbeitsmappe"  Bas0{FCFB3D2A-A0FA-1068-A738-08002B3371B5} zGlobalSpacAHFalse bCreatablPredeclaIdTru @@ExposeTemplateD0eriv@us tomiz BOp tion .licit P $ Sub Workbook_AddinInstall() ' This procedure adds an item to the Tools`menu 1 w(sheet bar. 'Aug 24, 2007$ frmTranswTextFile, Bowang Chen, DKFZ Ewill be s- .B Dim objCmdBrPp As CommandBarPopupPro8jec.A:AboutKButtonLOHst retch Hot=sh@S convert2@SNPHAPt[ LOVI EWZD HapMap2 2PedPhjLV#_ =np@'`2'IDseC,STR:OR_MantelHaenszel&0%^bJO`vrror Res:uNdagenerxr ruPn-tie"i>f!rpvzabsentZ' " `{nf_variref@ ing7 (~nS`qn= Appa!.(dos("Mr") ntr`d("R")d @ a c#w inbfourth >i D' LIf@"s e&d~, $C#Err.Numbe@r <> 0e_c}aHb.@( _b aType:=msoCoς#C#Wi G.J.Cac&!*End !C=(2-cdGa E ŢS& ( t'UL3^R___ QAO-b &^b]#sO"H"Bdd?d kG.BeginGroup51'?mOOKshowBIfJKImDisjsR[nhlepA VsGoTo 0Bl' p fuqnewc_BT @6 N"OFiV& ԠMSKmn&4??  Uk_HE@*=h8+3q3_MDv(IZxMESS S< < $<<<<<< <$<(<,<0<4<8N0{FCFB3D2A-A0FA-1068-A738-08002B3371B5}8  `HDaa X  % "xP(% &) T% (o th% *orks% ,@, 20% .j% 08faul% 2Xf% 4x% 6mmon% 8eck % :tion% <% >uest% Z`D  cro`%  o%es%   P`@`(hNR@@ @ @ p( @ @  @ `| @l @\ @L H `$ @ @ ( @ @  x ` `(~Pn " 0 &@ >h * 2 (08@HPX`h &p  *  * 84xX ,  ( 0(@8 x  VVVVVV8VXVxVVV HV@V` V   "  ,0Pp"(  "@h   $( 8Ph " @ X  p      " 2 &@ 0h  4|   x) This procedure adds an item to the Tools menu on the worksheet menu bar.r8Aug 24, 2007 add frmTransposeTextFile, Bowang Chen, DKFZ$ This will be set to the Tools menu.]@+ This will be set to the Project menu item."GetWi]`]]]]]] ]@]`]] Dim sep As CommandBarButtonWi]]]H# This generates a run-time error ifVal nI the menu item is absent.$ Create an object variable referring to the Tools menu. SendMSNPWorksheet Menu Bar B%D%F.l hW`,SKH&aploviewzHt 3B?;&pk1AS&rcE: *%Drtq& 2?3.paCo&mAltot`ys;YO8R (3pC)"0Ұ)B-:SЗ N of <`el@1.N7ernal t f +a#.OnAcᔠ="7S-Ygcu-9!0o-+.s-_- W- nvͱ2HAPLOVI EW" convertHapMap.OnAction = "C z2SNPh.Vtra@nspose,T output bPedPhase?d /, Compare\  'sep < xSTRJ OR_MantelHaenszelHTexptFil v'removeOldButton End Sub Private Workbook_AddinUninstall()6This procedure deletes an item the Tools@ menuw@sheet Bbar. ' If A Project comma&ex`ists,. On Error Resume N?Applhica.kB`ars("4M$")@ntrـ)("D2GD   (H " X 0+ , 8, 0X,$ " 0` , , 0,$ "   ,, @ ,H,`6P 0R   2D(` fh H $ "( P h  " $ "   " " "" * 08 " @HP X2Fp  2D$R $8 "Hpx  " 888 $R2D(2D`   " "p::8X (ZX(Z " &  0 @( h @x  &  0 2@ ,x *    (  00  0@  0P ` h  p  &x *- *0-    "       (V  (V  d  d     <=>k<1L9\Nh5hCuqԢ:9v^BlX.ƓLA}sLOY1[Fx}sLOY1[F<1L9\NMESPSSS<( 6"<< <$<(<,<0<4<8<<<@s (j axp@%(d`P  `@**Qj)( 0 ]h  iP $i f `x``  `>$ p ed.  @%2 To,@ `|@P 00{ iijp cationi End If   @% ) z @%`` 1H !0 `\` '*`$`p 蝄  $ ( @%` ame(`nNam ,H ` ==v)  !oH i zB@vi !``4``z( h`@ i`   .%  %"H80@"pTh@il"p@H@ (H 8  pHhH@ (H 8  pHH@ (H 8  pHH@ (H 8  pHH@ (H 8  pHH@ (H 8  pH05 #05"5( 5 h5xPN5` @  @ @ H @ x @ x @t 5Xp @l @\ 5X 5(TN5 5X`5(TN 5 pX5PhN5 @ @  @ 8 @ h @| l @h 5pd @b \ @Z 5T x 55p @ @ (@ @ 5|5 X @ @ @ @ 5( 5 p5hjnLx @  @ `p5 @5x`hRT5Hh|t50 @  8  p @ @ @ @ hRThH5@ 5( @ P8h! 5P.JhH @!@ 5( @ @ @  `!   0!X! `!p!@ @x !h 0!!d !!` !"5p`#5XP @@ 50 @, 0`$#5p.Jh# x$@ x$( @ @ @ #`x$## $ $ ($8$ P$`$  %@%HP@% @ @ @ @p @` X&P 0%X% h%L %%%H %%%D %)&@ %)%,.H&5X0 @ 5 @  xX'H'5h'4X'( PX'5 X@x+(5PH(P @X( ( %(((( ( ( X) h)p @ @) @ ) ) () )) * *@| @x @t (*8*p P* `*l **(h @d **` **+ +\ (+#H+X 8+#`+% p+T +(+P 0 +(*5L @H (5p8 x,@( @ 5 @  0 P @0x-5-P P- - %--- - (- P. `.p @ 8. @ . x. . .. .. ./| /(/x X/h/(t @p / /l /X/(h @d // 0`  0@0\ 00!5P5X @T 5XD 1@4 @$ P5 8@  P P 1@2 25 1 5`%5P581 5 %50222Hx20p2 2222( @ 23 35 3@ @ 5 @ 5| ,0  `4x45 54444 4 5 4 j@05 55 05`5 55` 555 45P6p5` 6H 70 @  7P5 4`5X (w8(  $@ H5  H p @$\ x~P(*\Rffff*0z50812abd\0$*\Rffff*0z50812abd$*\Rffff*0:509257c3 $R0  $X  $h ,x      "   &    0 $D8 ` ,h B *R ,L  F  F 0 @ 0H 8X < " $T$f0 Xp ,x 6 6 \ $x\ (@ H P`h,jp"   &$D@ ,HB`*Rp,L F F    0( 88 <p $ $ 8B( *p" 2*p0H Xp ,x 6 6 t $8\ " 2 T@    ,j8@ "  H 6P"   (HP$X  p 4Z   ( 4@ `p  8X * 4 8PHfX    " (  @P ` (  $j ("  0 8X$`  x 4Z   (( HX h 8X N( 8 H X "h (   $j 0 8 B  @ "H p           ! ! !(!@!X! h!p!$!*!$*!,R!6d",ZP" &J"&J"&J" *H"*H(#*HX# ,H#,H#,H#$($ 0$@$ H$ B  P$X$h$  p$ $ $ $$ $ $$ $Ph% `% p% x% H% .% % & 8& X& $`& (& & ,& & ' 0' 8' P' 0h' B' ' ' 0( 8( X( `( p( 2( ( ( <( 8) P) `) $) ) $) ) * B* `* p* "  ** * ** * * ** * 0+ +  + (+ 0+8+ @+ "`+ "p++ 8+ N+ + ++++ h-x]  *.nam, *.dat]H*.outab ]ps* CommonDialog2.fileName = TextBox2.Text !P(@iPoH !P(@o(]h] SNPHAP.EXE 'z($$h -nf $ '.Rkx$$h  $ 'd8$ was not created. PErrorA@Fk  $  $ '  $'!d$ (Failure running SNPHAP.exe. PInfoA@XdX` MsgBox "SNPHAP.exe was run. Check for the outputs when the task ends.", vbOKOnly, "Info"A If FileExists(outName(1)) And FileExists(outName(2)) Then !N(@ ReadResult_Click. End If Endk80o( !P(@o 5P(@5R(@ 5T(@, .Cel9N# .OptionButton2.Value = TruevbTab qo]X]p Convert_Click WinSNPHAP $ $' Smapl  $'olumn Failure running SNPHAP.exe. PInfoA@ d$$h$$h map !N(@k ReadResult_Click kHk@ B@o($$A@ $$A@Please$$A@ P$$$A@ $.trans$_transA@iew.ja$.trans$_transA@loview B@.jar") Endo t!d$r.dat |(dase co t!d+Only |!d+ She$\$rsnphap_warnings +$$r.out1 +$$r.out2 +oSNP tools: convert SNPHAP (Pat d(f8) If Val(Application.Version) >= 9 Then9 wHandle = FindWindow("ThunderDFrame", Me.Caption) Else9 wHandle = FindWindow("ThunderXFrame", Me.Caption) End If If wHandle = 0 Then Exit Sub hIcon = Image1.Picture* SendMessage wHandle, &H80, True, hIcon+ SendMessage wHandle, &H80, False, hIcon % frm = GetWindowLong(wHandle, -20)ed. frm = frm And Not &H1# SetWindowLong wHandle, -20, frm DrawMenuBar wHandleA@h j n!l9l n!9 n!p9p99fqH L( SNPHAP_Info+ SNPHAP_out1+ SNPHAP_out2+oHv If CheckValidName(Me.RefEdit1.Text) And CheckValidName(inName(1)) And CheckValidName(inName(2)) Then v9t$$hG$A@j$$hG$A@j |!d t!dA@ |!d |!dA@ 9tA@h$$h$$h5R(@5T(@& .ReadResult.Enabled = Truekq End Ifo z Gj] 8]Ph]] z z! %'*l8 *'$'* *$.. z$!0!'%蝄____ z$! '"(蝄___ z$!2'"____0 z$!4'%___0   J!1the original SNP from Affymetrix chip, all genome6selection includes SNPID,chromosome, location and SNPs   #SNP   A@h   7   7Gyj snpd(& the original data like Kerstin's one,/ fewer high density SNPs around 1 or two genes./ selection should include a colomn of sample ID  " #=snp listed in colomn, string from 1st col, the 0 col is blank  " A@h    7?b& vbTab & .Cells(rowStart0 + 1, colStart0 + i) 'SNPHAP doesn't require location snpkXqPV8l0 H!J % P saveSNPNameA@ o  z Gj]Ph]]] z z! %'*lX *'$'* *$.. z$!0!'%蝄____ z$! '"(蝄___ z$!2'"____0 z$!4'%___0   J! 1the original SNP from Affymetrix chip, all genome 6selection includes SNPID,chromosome, location and SNPs  " #sample  " A@h2 Print #1, Cells(rowStart0, colStart0 + j);  !%to start numbering with 1 for samples# For i = 1 To rowNo - 1 'SNP   'SNP      $$     $Gyj snp sampled( & the original data like Kerstin's one, / fewer high density SNPs around 1 or two genes. / selection should include a colomn of sample ID   #Usample 'SNP starting from the 3rd row (the 1st row is SNPID, the 2nd one is Location)   A@h    7@ sample ID;  " 'SNP      7$N If Len(.Cells(rowStart0 + j, colStart0 + i)) = 0 Then Exit For snp samplekqVl H!J % P saveSNPDataA@`oX0 Dim fileName1 As String, fileName2 As String]]] $' .trans' .trans'   A@   A@o8](@]X] $' '   $! > $! >$'>  Debug.Print longestl    HAP     > $ $ % $ str = SNPName(i) & vbTab- Print #1, i&; SNPName(i) & vbTab;  A@ $! G $!  %j    Probability    $!   Cumulative    $!  Vl H!J % PinfoA@xop]p    ] $' 'l   $! > $! >$'>      $!    > $ $ %   A@ $! G $!  %$j    Probability    $!  Vl H!J % PinfoA@ho`  Dim outIndex As Integer]  ] ]DP h   ] ]   outIndex = 1  'd)'k ' j$'  $'\  \  ' 8 '  \  $ '  $ '  GFj $  % $( $    % $( $  % $( $! %x $( $! %x $( $! %x $( $! $ $( $! $ $( $! $ $( $! $ $( $! $ $( $! $ $(  'p  'iP@ ]  ]0 '  Probability' Cumulative'dSubject' Probability'k   $  $ G  'j i(BPrivate Function ReadFileToStrings(fileName As String) As String()' Dim n As Long, i As Long, k As Long Dim arrBytes() As Byte Dim nLine As Long Dim myStr() As String On Error GoTo ErrorHandler" Open fileName For Binary As #1 n = LOF(1)& ReDim arrBytes(1 To n) As Byte Get #1, , arrBytes Close #1 nLine = 0 For i = 1 To n)' Debug.Print VBA.Chr(arrBytes(i));< If arrBytes(i) = VBA.ASC(vbLf) Then nLine = nLine + 1 Next i' Debug.Print*' Debug.Print "Number of Line=" & nLine ReDim myStr(nLine) k = 1 For i = 1 To n+ If arrBytes(i) = VBA.ASC(vbLf) Then k = k + 1 Else6 myStr(k) = myStr(k) + VBA.Chr(arrBytes(i)) End If Next i' For i = 1 To nLine' Debug.Print myStr(i) ' Next i ReadFileToStrings = myStr GoTo out ErrorHandler:; MsgBox Error(Err.Number), vbOKOnly, "ReadFileToStrings"out: End FunctionH ] clear and init (f n9f9q j$@9 n!p9p999fqhd` setStatusBar (0) n(f (f j  n!9 d$%9P9fqkA@o* CommonDialog1.fileName = TextBox1.Text On Error GoTo out: CommonDialog1.ShowSave* TextBox1.Text = CommonDialog1.fileName On Error GoTo out: CommonDialog2.ShowSave* TextBox2.Text = CommonDialog2.fileName$ CommonDialog1.CancelError = Truealog2.$ CommonDialog2.CancelError = True,hX( `(@P``8( `@(`0Attribute VB_Name = "frmSNPHAP"  Bas|0{A2B0C113-D0A1-A448-B7C1-5FAF1DEB34CC}{4FB7D5E4-6729-4C4F-92F3-83A90684DA} cGlobalSpacnFalse CreatablPredeclaIdTru @Expo se.TemplateDerivCustomizBOption .licit Dim ing(2) As Sng '*.nam, *.datoutÀ shee1PRV Sub CommandButton2_CCk() '  onDialog1.file7GextBox1,.T O1rror GoTo  :ShowSaveA "Me.Convert.EnAP#FiEndA3 U63626262.6666C4HRetValADou@cmdǒB A@.EXE "CIf F}E@xists(1)) Then"!C+ "-n f " +eX1)s4IfB 2{ 2 |!aMsgIhg was not ced.", vbOKOnly, "E!V!GWH?*Op1)=`"J3= Shell(Norm@oFoxcusC#0k-"Failure runni#7exelInfoCE%{ % . Check fytheyputs w`> task endsR & k<%uJE?e.ReadResulf !b!D9_,A :> l䔠hange!W UserF=_A0ctivWith Me ?#΁$6Win]G%`#.c$.uB ?A III I^q7"6&WF &"Ps77B7b77E|711O1 (!UAO1O1`''qgaYHide),,Ud!2=ToNet1CbQ0), w03N1 12 Q9Wrots0rCs", G q&.transd _(_o\olBX7$J1_C)JLParseФe(u"lb&pB2 = 0)@':x\"snphap_warqmse= ome 1 s{2"/a[Initize`;jN!6Ca toolsh: c ) Image1.Vi|si`pHY C@X((Appa.Versp) >= 9V?wHindRdow("ThunderDFr@E+ ľہOHXOE0L@E` WSpithIPict c{SMes s` d, &H80, h, ?b GetLong(F|-2 J cQqYNot1  , CDrawMenuBar% 1setStahtus0""Percent#.Top progKLeft!Heigh-CGWid= r=(Ab2 OptionButton2.Value = True ' CommonDialog1.CancelError2JsheetName(0)z"SNPHAP_Info" 1 out1 2 2" End Sub Private Convert_Cl ick()If@ CheckidGMe.RefEdit1.Te`xt) _HJA+ in1)B2Then)On Resume N9Wit0h MeA.MousePoin$tefm HourGlassrFileExi0sts(YE Kill E1@ savey%K W, AYBox[ Data 2h HDefaultetStatusBar 0VNTFBm.Enabled́.WinOW  @adltYAIf#AoCA e(6(SJce As String, vfI) %= "" Or"MGoTo @x Dim iALo jGsrc  rowNo8col9rt~0 KA AaW8ork⒢= VBA.Lefta , In"!") - 1C Bfz{Hand8ler Re@place(,P "'"" Set B= SsD#C"= Range).Rows.Count '蝄___c'/ C > (m  '____h@ TColumnB"Open#FF@Output2#1!"Aa;`N1Mf'the original k from AffymeYx chip, agenom''selec include@`NPID,ch`os, locab< i ~0 _%`VE\ 'FzsIi / (=<#1, .C0ellsa.+ 8i, f0O&Len(u` k cP !G Y W_AB_Code(_|Y|^j)|/}@ Next i 'snp (Print #1, "" pjh ample4Els' the original data like Kerstin's one, [' fewer high density SNPs aro und 1P two genes. ReadFy ToJff=& ".transfg2Xj0Rot1[(\, $2/2&2f8 8e 7- n!) bF/Lon =jCnlin@leBmyHdap#.haca strg @0rF0fin, 1#/C= UB(jb%=` IIf(A(i). ID) > d,", $Zebug. /DOu^ bwBsvpfa/aOutputA##1! 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SNPDataCor0Base  B|__SRP_aG__SRP_bbN      ( @ X x      , 0 P *h   ,   .( X p " " " " "  "  (0" 8 "@ "P ` p "B@  "  B ( (B 0$8 PBX` xB B   <=) dle =  %i  tion),0`@ X\am) End If %i  Sub,$`@p \_ &i  SendMe,`@ `bdoi   ,`@0 defri  Bar wHxPl%b4@b8@(b(@ @oXx8 0x(8Text%` Xx8 0x(8p Xx8 0x(8 Xx8 0x(8 8`8 8 8`8 8 8`8 88` 8 88`888h8X 888H8X`8p8X @ 8 00hH88X80@8 @ @ @ @ @ @ X @  @ 8x @8(8 (`(`@8x 8 P8(8 HH`8x 8 p8(8 hh8` 8 8pp8 8 @ P8h 8  xX xP(PP% ~Pk  ( B08 @BHP XB`h pBx B>' x]@]@]@]@]@(x 'i8 'i 8 'i 'ip 'iXProperty Get getSNPid() getSNPid = SNPid End PropertyProperty Get getCH() getCH = CH End PropertyProperty Get getLoc() getLoc = Loc End PropertyProperty Get getComp()  getComp = Comp End Property&Property Set SNPid(newSNPid As String)t, L SNPid = newSNPidest)1) End Property#Property Set letCH(newCH As String) CH = newCH End Property%Property Set letLoc(newLoc As String) Loc = newLoc End Property'Property Set letComp(newComp As String) Comp = newComp End PropertyX 'o` 'oH 'o0x 'o 'o8 ' ' ' ' 'o !' !' !'(j !'B@v !'!joh , , , , 'i[  !o   %'i  %'i0  %$'$$i  %'iX  %'8i0(xAttribute VB_Name = "SNP@Data" Bast0{FCFB3D2A-A0FA-1068-A738-08002B3371B5} zGlobaBlSpacFalse Cre wblPredeclaIdAExposeTemplate Deriv$Customiza COption .licit P $ ID AHs Sng C"h Loc Lo omp Boolean Geno + FuncAget:id(z)  J 0End CHCH@Ch / 04= @/89C>= WGBCB, ' 'Property Get L 'P 'J AKFIH C() @@BJG )b 9SetnA"a!" bHl$Sub se@N#AxbbI  1!|H-ae) !@ %e) M`A)-Ab"!& Pub Da!G,EI@A'@$, Cal6a .) Q ab oOFromd) .Ech5`CH  "$f1FɻB=qS" (& "," & 'EA% `ا@)lntr )2 Debug.RSr# Equal2 Y! (5())" P p= (4AR1V IsHomosSsS_f.Gjo 6xNoCallIs  Mpeterm H 13232(*\Rffff*1350813232\0 d  (08 B  @@HhB  p@x B  . ,   ( @  "Px$   $  B   ( 0 B  8 :@   6.6   ( B  08 @H$Ph x  z374dfkexRRMEd @@6<(""0L6      ( 0 8 @ H P X ` &h         x 2 " H P X 4j`   B            ( B  0 8 ,@ X *p 2 $ <@  (H :p > 0 4  *X p.x *22202h222 H X`hp,jx B       (B  08FH`x B    &6    "    X 0X F:l &.8 @P B  X 6` , H   8 P b` V   0 BH F \ 8 &P "x ( $     &( &P x *    . (0 "X $ 4 2  0 P h  " f   028 p >x 4 : 60h  $ "0 (X " 6   " 0 P B  `8hx B  8 x^^0^H^`p@x    $'i    $'bli`x' Returns a string containing the binaryv& representation of a positive integer.]]! Make sure value is not negative. ' Construct the binary value._  X '  '   Add leading zeros if needed.8   '" " "0$\ '  k 'Ji(3 Returns the decimal equivalent of a binary number.]]]] $'* & * $ & %'(  (1G  * &  ' j 'Hi]H'0_ . 0'0x .'. . 0',ih` 2$'bi8] 8* p!'  = sheetName = VBA.Mid(myStr, at1 + 1, Len(myStr) - at1) p  %'k $-6 p  p- p+ p* p/ p# p$     " p"* is not a valid (path) name for SNP tools. 1Please don't use sheet name starting with number, <and don't use space, '#', '+' and '-' in sheet or file name. Please change and try again. PErrorA@'4d'4kiP '6  %'  %|'   $'6k0i(]0H`]x]]l j $:' 8 8JV P'  p( Debug.Print VBA.Chr(arrBytes(i)); $8 > %<G  'j   Debug.Print) Debug.Print "Number of Line=" & nLine p8'    $8 > %<$  'dP $p $8 % +pk  $ For i = 1 To nLine Debug.Print myStr(i)$ Next i p'l H!J % PReadFileToStringsA@ XiP@]]]  @ B%..B H!J F!$FD B!.%L.B @ B(kl BB@H$B@H B@H G:\Chen\Data\SNP\SNPHAP\snp.out1 TEXT; jNA1$P J!L%L .Name = "snp_1"9R9T9V9X9Z ^9\9`9b9d9f9h .TextFilePlatform = 9369j n9l r9p9t9v9x9z9|D9~, .TextFileTrailingMinusNumbers = TrueC@BackgroundQuery:=Falseql H!J % PreadTextFileToSheetA@`oX(]'     B'   'ki] !*Gj]$ Dim rowNo As Long, colNo As Long, Dim rowStart0 As Long, colStart0 As Long Dim srcSheet As Worksheet5 srcStr = VBA.Left(Source, InStr(Source, "!") - 1)l! Set srcSheet = Sheets(srcStr)4 rowNo = Range(Source).Rows.Count '蝄____7 colNo = Range(Source).Count / rowNo '蝄___* rowStart0 = Range(Source).row '____0- colStart0 = Range(Source).Column '___0 !(   5 $Dim myPed(i + 1) As New PedigreeItem5  5 5%  $(5  5 5%  $(5  5 5%  $(5  5 5%  $(5  5 5%  $(5  5 5%  $(5  5 5%  $( q 'Fl H!J % P readPedigreeA@PiH0 ] '   p $'y k i  ]h  ,$' p $'i  ]@ ]X '  8! p !'y( k  i x Q to mark the id in a range with red backcolor if it is missing in the other range* usage format_missing "b2:b101", "g2:g101"? the id in "b2:b101" will red if it does not exist in "g2:g101"]  $ ! $$ !^(`)red=3, yellow=27k o  / to replace a substring in myStr with toreplBowang/DKFZ, Dec 06,2007 p  $'i( APublic Sub transposeTextFile(inFile As String, outFile As String)'August 16, 2007 'Bowang Chen'DKFZ['to transpose a very big text matrix for Stefan. The maxtrix is too big to fit in MS-Excel.P'we read a externel text file, transpose it and save also to rxternal text file.'usage:'transposeTextFile< Dim i As Long, j As Long, nline As Long, ncolumn As Long? Dim myline As String, lines() As String, splits() As StringV' Debug.Print "We assume the separator is ',' otherwise please modify accordingly." nline = 0 Open inFile For Input As #1 Do While Not EOF(1)! Line Input #1, myline nline = nline + 1 Loop Close #1 ReDim lines(nline) As String Open inFile For Input As #1 For i = 1 To nline# Line Input #1, lines(i) Next i Close #1( ncolumn = UBound(Split(myline, ","))! Open outFile For Output As #2 For j = 0 To ncolumn For i = 1 To nline- splits = Split(lines(i), ","), Print #2, splits(j) & vbTab; Next i Print #2, "" Next j Close #2End SubPrivate Sub Command1_Click()` Create_ShortCut "C:\WINDOWS\NOTEPAD.EXE", "Desktop", "Notepad", "test arg", , WshNormalFocusEnd SubAPrivate Sub Create_ShortCut(ByVal sTargetPath As String, ByVal sShortCutPath As String, ByVal sShortCutName As String,'Optional ByVal sArguments As String, Optional ByVal sWorkPath As String,'Optional ByVal eWinStyle As WshWindowStyle = vbNormalFocus, Optional ByVal iIconNum As Integer)8' Requires reference to Windows Script Host Object Model- Dim oShell As IWshRuntimeLibrary.WshShell3 Dim oShortCut As IWshRuntimeLibrary.WshShortcut0 Set oShell = New IWshRuntimeLibrary.WshShellv Set oShortCut = oShell.CreateShortcut(oShell.SpecialFolders(sShortCutPath) &' "\" & sShortCutName & ".lnk") With oShortCut .TargetPath = sTargetPath .Arguments = sArguments! .WorkingDirectory = sWorkPath .WindowStyle = eWinStyle0 .IconLocation = sTargetPath & "," & iIconNum .Save End With Set oShortCut = Nothing Set oShell = NothingEnd Sub !!`'i !^!`'i`X````0``X`h `x` ` V `PA `A `  ` {|` {`|`v`H``xH0pBAttribute VB_Name = "Base" Option Explicit ' Type stretchInfo Ch As LongLengtA $Start HE\nd X Pubk Func{Max(v1*Variant,( v2) Do5e|/IIf-5>+/13) fW ginci3in3<34DecimalToBinary(`Valuee, Minimum@Digits I@ntegerwS؀w' Ret@urns aing contathe b3represeofpositive i. Dim &86hd=  &\ 2 Loop While> 0' Add leadAezeros if_=JC* Q=- (2CBIf@働_@ ThenB J?Cn(N, "0"l dIfb V^#j ]\To(]Z/‡b GZ;d1 equiG@W VZ number)q!Sidxhf tmpB{B@^dMoD=2(C3For = To 1 Step -1 A a= A.Mid",, 1 A`="1";Er=+ 2 ^ ( -!NextBC1'9 8`,N+(By`6 se%a,c _@,(-"Dte ssfb =rUntilF=r&' MoOrBU(vIɜ "`08j M Check@ id,my'q,Boo#{,atb!V, she"@.p" 4raamid (path) naЙfESNP t !s."PvbCrLf W!& "P #se donp't uSsCqiwithTT,o0apace, '#'@+' '-' ( @ fq! O dD changertry ag ."bOKOnlyp+ErrorC3 7Fal:sCEpTrud ':c g9umS56(-6?PNPf,.VB 0 ThenK!O.Add(Af ter:=qs(.Count)׃8*.=;End IfsGoToTorHandler.Select Cells(1, 1) .clea'G:\Cu\Data\SNPHAP\sn@p.out1&With ActiveBO.QueryTables>0Conn@W:= _ 8"TEX@T;" & E, Destinb:=Range("A1"F' EC"!_1". FieldJs @= TrueR owoFalslAdjacentFormulaP PreseHrveAat(gef hOnðOpen@R Style@xl$In@tD@ftee,SavePasswordOAAe@:2ustColumnWidfC!Perio A0PromptOn+aF 0latf&@936/ Start/EB8arseTyp! imitedQualifip= x"l*DouMQu 1k +Da %!.#)Pedigree(sre!s"Info `Item("m y("New  .src  ""B q Lj5C+~No@6ZrE0+ wV *Left(Source,`&"!") -r ?w:wa=6 u)#= Ssn).Rs '蝄____S3] / 3>$ '____0F) e9ReC$`.o "No&‚56po .'wi 1*p,.FamilyIQn+a .Ï" i, .`=0 PGivdid`hID/orwrt2 Father l2 a.Mok 3G~eSrQ~p4cAff tuQkOOD5OBLiabmtyC?s(/&63AU iUmTR RUNjoooom`ooUn]?onB~`Of(myQWm>yB1p~Bozo`nB 3nI }8UB1O'P`C= i)_mQ5Exit $n:,E aO(g tp:S@tC ,"OfF )r`o  cSNVrBInb a EachPrI~nsDY ضyCell.Value Then InRangeOf = True pExit For(End IfNext Function Public Sub format_mis sing(b1 @As Str, 2) ' ' to mark the id in a r with red backcolor if is e.8or6RusageG "b2:b101", "g2|:g?;clq Each In)If N-=($܄2))Inter ior.CIndex3 'N =3, y&ow=27LtB(uqN txBplp(,my@Go,@nfindKreplG>)Z;{Aace@ysubsTC|to 'Bow/DKFZ, Dec 06p,2001#= R'E%R) 'ts poseTFi`le(in-,0 out'Augu16, %#'* CA''qA, '';;very big nt>xefan.wxtoo o fn MS-Ex%|.wefad@ernel^f1?6ea4sDav@.lsomrrx Fna(! f:/"c7\ia#Lo ng, jGnline`uumnmy 7Bs(D, splitj@!eDebug.P`t "Wssume@separaF !&',' wise pleamodify a ccord@ly."= 0pOpenQ>AxInputA#1aBo Wh-BwEpOF(1BeL"C#1, '+ LoopClS ARe0&.l i1 To~  a ih imn?= UBound<(S!:s,")$ b%laOut-2'!j0 !aJ?e L#2Rj) & vbTab;i!!"L"j&ASub r ivateCoDmm w1_Ck"(D&Cre_S hortCS"C:\WINDOWS\NOTEPA D.EXEDesktopf2dteKarg, WshNQ{lFocus 'pyK(By sT`etPaPzX~  Na <_ 'OpIArgp>8ntsQ8CMWo rkeWinpStylJd4ow=, ,iIconNumQ!wger0I@Requir0referenm_Џcript HopObject Modelc Qp  (p@  (lh    <p  (p  (l 0  @H2*P ( >   ( B0 .x * 2 2 TH : 0   88 8p ( (  : >@ 0 4 0 4 P X :p 6 < ( 6@ 6x 6 8   8 @ >` N   6( ` :h : : <( h Lp  R >8 @x  P >( @h    4 8 X "x  "  \ X x      xPrivate Declare Function FindWindow Lib "user32" Alias' "FindWindowA" (ByVal lpClassName As String, ByVal' lpWindowName As String) As Long5Private Declare Function GetWindowLong Lib "user32" Alias' "GetWindowLongA" (ByVal hWnd As Long, ByVal nIndex' As Long) As LongPrivate Declare Function SetWindowLong Lib "user32" Alias' "SetWindowLongA" (ByVal hWnd As Long, ByVal nIndex' As Long, ByVal dwNewLong As Long) As LongPrivate Declare Function SendMessage Lib "user32" Alias' "SendMessageA" (ByVal hWnd As Long, ByVal wMsg As Long,' ByVal wParam As Integer, ByVal lParam As Long) As LongTPrivate Declare Function DrawMenuBar Lib "user32" (ByVal' hWnd As Long) As LongPrivate wHandle As LongSNP tools: hotspot (P d(fA@h j n!l9l n!9 n!p9pingM99fqox@! CommandButton2.Enabled = True v9t |z ~A@Te 9tA@hC@qo"Private Sub CommandButton2_Click()! CommandButton1.Enabled = True" CommandButton2.Enabled = FalseEnd Sub] clear and init (f$  n9f9q j$@90 n!p9pStar999fqXdP setStatusBar (0) n(fPrivat (fFuncti j  n!9 Alias d$%9P9fqkA@oPThis macro finds the break point from one region to other on the same chromosomengusage:" Al1. run the macro FindHotspot()nd AU2. select the data area includeing 4 columns: SNP_ID, Ch, Loction and comparisonValuencti&3. tell the macro where to put result.etWi 4. click RUNhWnd A)Bowang Chen, DKFZ, 29.07.2004, 09.08.2004]x]]]0H]`x]] z z! %'* ~ ~! %', *$.. ,$.. z$!0!'%蝄____ z$! '"(蝄___ z$!2'"____0 z$!4'%___0 ~$!2'$"____1 ~$!4'&%___1 SNP ID $ & ;Ch $ & ;Location $ & ;q8 With srcSheet'   %   %   %   %$B@ End With'   6 If Not frmHotspots.CommandButton2.Enabled ThenF MsgBox "User stoped.", vbInformation + vbOKOnly, "Hotspot" Exit For End If   A@h  -    %    %    %    %$B@$$%$$% new point found $! $  & ;Ethe start point$! $  & ;$! $  & ;  '$! $  & ;E the end point$! $  & ;$! $  & ;  'q8k0$$B@#store rurrent SNP   G  'j B@H $ &$ $   & $ %B@H Selection.CopyoX;Public Sub FindHotspot1(Source As String, Target As String)' Dim i As Long, j As Long, k As Long$ Dim rowNo As Long, colNo As Long, Dim rowStart0 As Long, colStart0 As Long, Dim rowStart1 As Long, colStart1 As LongN Dim SNP(2) As String, CH(2) As String, Loc(2) As String, Comp(2) As String4 Dim srcSheet As Worksheet, rstSheet As Worksheet* Dim srcStr As String, rstStr As String On Error Resume Next1 srcStr = Left(Source, InStr(Source, "!") - 1)1 rstStr = Left(Target, InStr(Target, "!") - 1)! Set srcSheet = Sheets(srcStr)! Set rstSheet = Sheets(rstStr)4 rowNo = Range(Source).Rows.Count '蝄____7 colNo = Range(Source).Count / rowNo '蝄___* rowStart0 = Range(Source).row '____0- colStart0 = Range(Source).Column '___0* rowStart1 = Range(Target).row '____1- colStart1 = Range(Target).Column '___1 With rstSheet3 .Cells(rowStart1, colStart1 + 0) = "SNP ID"/ .Cells(rowStart1, colStart1 + 1) = "Ch"5 .Cells(rowStart1, colStart1 + 2) = "Location" End With0 SNP(1) = Cells(rowStart0, colStart0 + 0)/ CH(1) = Cells(rowStart0, colStart0 + 1)0 Loc(1) = Cells(rowStart0, colStart0 + 2)1 Comp(1) = Cells(rowStart0, colStart0 + 3) k = 1 For i = 1 To rowNo - 17' If Not frmHotspots.CommandButton2.Enabled ThenG' MsgBox "User stoped.", vbInformation + vbOKOnly, "Hotspot"' Exit For' End If0 frmHotspots.setStatusBar i / (rowNo - 1)4 SNP(2) = Cells(rowStart0 + i, colStart0 + 0)3 CH(2) = Cells(rowStart0 + i, colStart0 + 1)4 Loc(2) = Cells(rowStart0 + i, colStart0 + 2)5 Comp(2) = Cells(rowStart0 + i, colStart0 + 3)E If Comp(1) <> Comp(2) And CH(1) = CH(2) Then 'new point found With rstSheetK .Cells(rowStart1 + k, colStart1 + 0) = SNP(1) 'the start point8 .Cells(rowStart1 + k, colStart1 + 1) = CH(1)9 .Cells(rowStart1 + k, colStart1 + 2) = Loc(1) k = k + 1I .Cells(rowStart1 + k, colStart1 + 0) = SNP(2) 'the end point8 .Cells(rowStart1 + k, colStart1 + 1) = CH(2)9 .Cells(rowStart1 + k, colStart1 + 2) = Loc(2) k = k + 2 End With End If- SNP(1) = SNP(2) 'store rurrent SNP CH(1) = CH(2) Loc(1) = Loc(2) Comp(1) = Comp(2) Next i If k > 1 Then k = k - 1 rstSheet.SelectV Range(Cells(rowStart1, colStart1), Cells(rowStart1 + k - 1, colStart1 + 2)).Select' Selection.CopyEnd SubH x<Attribute VB_Name = "frm Hotsp"  Bas0{1C8BD336-4DA6-2D42-8700-DD47021508C7}{9C1 074A9@15-234F-AA45-6B6EE1B3DABD} cGlobalSpacnFalse CreatablPredeclaIdTru @Expo se.TemplateDerivCustomizBOption .licit0 'P!% DAG FuncFindWow Lib "user32" Alias _ ' "A" (ByVal lpClassAs Sang, l&p/ ) Long 'NGetA ( (hWnd&nIndex7D"$S$ $E,dwNew@*ndMessag2eOSe )wMsgSx|wParamInteger/l0YDrawMenuBarkOf)s(,B+( 0) "@5 IDWS?1 + "1Chow;;pLocaS?Wbh # P (1).iD1O& p`w!,w _ srcSheet.Cells(rowStart0, col( + 1) ,628v3) 'End Withk = 1 AFor i To No -#?CIf Not frmHotsp.CommandButton2.Enabled Then;MsgBox "User stoped.", vbInfor@mationvbOKOnly, "1"#Exit T lIfdsettusBaf/ ȃd)SNP(2).DataЕ)iKw0NhOO@gC@x(xE1).Equal xp(I)) A{JH}'new poinoundp rstJ 1̀[k[0)@D!Bg{NPid'xtheCl1)KCH2Loc nk`n Te1,_(Fc _ 0FU>2N,w:dqFrom A` ' re rurreI" Next iB Wk > 1=P c-a,L.S`electfRange(k1M {QkR2)) c `py !aSub ' 'Public A FindD1(Source As String, Tar>'1ĹDim@LojCkE#C)K1'F8 CHa`H,? Works,Ɖytr@) `3!FOn ErrResume M= Left, In"!")"D$%,Set 6= 2Rs(T!PqЇUtr  = C.%).RowsP)u4'蝄___._S"]C \t /" '___\_0F/) lhumn1 ).1CohY ?rY"- IDHOw1a "ChmE1dD1 +6B]JL0#8_':2)omp(/-%Q [fQ5 '@_m^@'f0)m/j+O= ,0 OާWsUO+ L1t0oo+ !7 `]!<> f^F)aQ 'MFA;Q28 oU Σz 0PH.q"5S@C  o 7pGB%OONf 9#e 2OM]4vNJ$  )LA i ' If k > 1 T(henP=- 1rstSheet.SelectPRange(Cells(rowStart1, col), 9 8 +H$2))Wdion.Copy 'End Sub ' n@!F"!") - 1)B D5H C*E EK S'y{= vs(C If Err.Number <> 0 TheDn LAppa.Act@& ' ,HA= .%).Rows.Count '蝄____T/ NW%R0v   '____0E Z lumn 1 74). 1 OCo? #SK\` T End Sub  ia@\٧)  /MYw 'a7qAL P @, dTP @, dXPwTniid40(i8nBii@4PwXniid80(i80Bii@8VhniiPi<Thnii.r<. @J hnii@DJ hniiHJ hnii@LJ hniiPm D$ 4 8 < @ D H L P T X  f=rU h,`u00 @4 @(8 @4< @<@ @DD)@LHI@TLi@\P@dT @lXnAffy_anno_gene8* __SRP_6 __SRP_7frmTransposeTextFile*,%x ($ %x ( !/ !/ !' (dXNumber of fields =  (k(o  ``xAttribute VB_Name = "Affy_anno_g ene" Bas0{FCFB3D2A-A0FA-1068-A738-08002B3371B5} zGlobal!SpacFalse bCreatablPre declaId)     !"#$%&<*+,-.801234567(9:;=a@ZBCDEOGHIJKLMNPQRSTUVWXY?[\]^_`cpefghijklmnobqrstuvwxyz{|}~(  . `k@SdK^L$>s*=h8+3qq @]xq @]K^L$>sME8 SS S0(>"LLLPLL<<<N0{FCFB3D2A-A0FA-1068-A738-08002B3371B5}%( %*,.HB %jPDD@j$LT@j&xP\@j,Xl @  `0o@t iz` $i~$%*4@ob*8(8@j(<4@j"@@<@jhHL@j*Td@@h(Px@h(PxX@h(Px@h(PxX@h(Px@h(PxX`@<`x@4  !8@hD x !8@L`x `X@(` (@  px@ @ @ 8@ @ @  @`H "$&@  hx0@~P*\R1*#21b$*\Rffff*1150812abd*\R1*#142*\R1*#140*\R0*#19*\R0*#13*\R1*#14d*\R1*#145*\R1*#151*\R1*#21c*\R0*#f\ ! (08@HP " X &x$P$PP"rP0"r@ *Vh,T J J J J(  "Hp x] ] ] ] (] @] P] h] ] x] >As stretchInfo Dim myRange As New rangeInfoX z z! %'* ~ ~! %', *$.. H!JG B!J.j ,$.. H!JG B!J.j z$!0!'%蝄____ z$! '"(蝄___ z$!2'"____0 z$!4'%___0 ~$!2'$"____1 ~$!4'&%___1 getstretchInfo = myRange joP`0Hxp       ! `0Attribute VB_Name = "rangeInfo"  Bas|0{FCFB3D2A-A0FA-1068-A738-08002B3371B5} zGlobalSpacAFalse bCreatablPredeclaIdAExposeTemplateDeriv$Customiz COption .licit Pub srcSheet As WorksrstowNBoLongcol rowStpart0 1 1tr S$0E*Sub getstretch(Souru@B, TarcG) '@  ' Dim myR New* Ơ O@^rror Resu0Next-= VBA.LeftaD!, IAExposeTemplat@eDerivCustomiz COption .licit 'Bowang Chen 'June 18, 2008 'to de$fi a Vss foe the mex Dta*of  'Values o a list  s which!SNP i ssocifd 7 (separby ///). 'for ea2.Transcript a ccess6// - reIship d"$an@m(v( 0 if with,in$ ) UnDiG@ Cl@Qe0r IDAna"symbolNCBI BankO' ? TM_CNGNDC_cwDCF_FG_G_GNJ_deEJ  tagb0riefub setaFse<#!g) Dim "As()h CtSplit @, "//" If UBounds)6a>nf Q Me.5=A@im(0) w$.81:2-==#3g>/ 4/ @/5/qCf6 B= @-'&5" &(he%m6P"E!2e Numbfields =Cnd If ESub rU 88a@X٧)  /i7q!?y70   4 8 < @ D H L P T ZKrU d(a`e 0 I @4 @$8 @,< @4@ @<D @DHA @LLq @TP @\TnrU 8 ~P " 0   0  " 0H x 0 $(8@ "H$P` "h p "x  "2   $  &H *p    $ * *  : :0:H *`:p:: * "HH  (,f8 "h x B     <  fk`Ꚅ=CˎE8G"*=h8+3qMl?F!E)xMl?F!E)Ꚅ=CˎE8G"MEPSS S6"<<<<N0{FCFB3D2A-A0FA-1068-A738-08002B3371B5} j<,@jPD<@jHD@j@PT@ % `Jdi hPp%j4@j8$@j(@4@jxLL@jT\@hPx@(Px@(Px@(Px@(Px@(Px@((\ 8`Hx0 ( @ @ xh X@H X@ x@(xX@ 0 A8@8xX@@ A8@@HhxH@P( @(  h  @@$p p  @ @ @ @  @  p@pdh,~P$*\Rffff*1050812abdX!   >8 lx ( "  08F@X Bh B B  B B B  0t@ p (. x Bowang Chen June 18, 20087to define a class foe the Affymetrix annotation of genefValues are a list of genes which the SNP is associated to (separated by ///). Values for each gene are Transcript accession // SNP-gene relationship // distance (value 0 if within the gene) // UniGene Cluster ID // gene name or symbol // NCBI Gene ID // GenBank description? The SNP could be within the gene region or be upstream or downstream of the genes.] ] ] ] ] (] P] ] x] @]8 //$'in $ %x ( u$ %x (ns$ %x (en$ ($ %x ($ $x+$%ka$I#p\NNn@F(MxԹ}e{KU?oeϝ'CMxME@SPSSS`@p//Uiii i````` p 0(%X0 %0@@%f%@0@@0@@0@@ p(p p(p ``( x   ` @   ( ` ( @ h vtPt| @  @ @ (@  ( @ h h     h8hP @ p   @ @ @ 8H x( @   "  "p @ @ @ @ 0 o $s $w `0 '? )? 00      " ( 0 H ` `p V ( 8Pp \ .$L(8 H Xh p< &  > "  8 H X hx B  ," @ P ` ,p  X x0o(@ !P(@3PoH !P(@o( 5P(@E00qo%SNP tools: transpose an external file (P d(f setStatusBar 0 With Percent .Top = progressBar.Top .Left = progressBar.Left$ .Height = progressBar.Height .Width = 0 .Visible = False End With OptionButton1.Value = True ,5B@TAB5B@{space}5B@5(,5B@TAB5B@{space}5B@5(qo@] !!$' !!$' v (t P(@ t!d |!d  A@>?",", "," P(@  (t B@o ,KT,'{space}KT 'TABKT 'S` 'nPiH0August 16-24, 2007 Bowang ChenDKFZZto transpose a very big text matrix for Stefan. The maxtrix is too big to fit in MS-Excel.Owe read a externel text file, transpose it and save also to rxternal text file.usage:transposeTextFile] 8 ]PhU Debug.Print "We assume the separator is ',' otherwise please modify accordingly."' B(Reading ... B( $b   'V  $'        $'   $  +  V   Writing :   /   B(    $   G j8vbTab;   B(Vo* CommonDialog1.fileName = TextBox1.Text On Error GoTo out: CommonDialog1.ShowOpen* TextBox1.Text = CommonDialog1.fileName* CommonDialog2.fileName = TextBox2.Text On Error GoTo out: CommonDialog2.ShowSave* TextBox2.Text = CommonDialog2.fileName0 $ CommonDialog1.CancelError = TrueleName$ CommonDialog2.CancelError = True xAttribute VB_Name = "frmTransposeTextFile" Bas0{64FDE7AA-76D4-B940-A7C1-C0C15096A1F7}{D8F4C035-ECC8-454F-AE09-6C90890C 7E91} cGlobalSpacnFalse CreatablPredeclaIdTru9 @Exs .TemplateDeriveCus tomizBOp tion .licit P $ Sub CommandButt on2_Ck(0) ' onDialog1.fˁBox1.O0rror GoTo out:!ShowOpen #b End+/3/2/2,/2./Save / / QMe.Convert.EnfAo6 fG@ehangee[HUserForm_Activ}With Me((CA C Initiz+Resu6NDaSNP tools: t} an @ernal O"Image1.0VisiIm2setStatusB0ar 0cPe`rcent#Top6progr4es. Left A(HeighmWid-=bmf,ǃvraluFkeCancelEp= 2.G$+Ambo{AddItem ",/@TABy{s!ListIndex-0b< 2.2.2`zfADim DLM1 AsD Sng,2B= which`(ƒ%.V!=)2@"2.MousePo inter@fm HourGlass /|fo!Av D#,1D'@D,Dԝ$Default !HideVGFun@Ll6selectedw),Sb C*#a).e"$ #0(XvbTabWEQa1hO B(b  q(jy Qci, j)(j! jiHOut2Q mn*j(Wrngb(ep(:j !)"/Q*i"C68#2, ; If i *=h8+3qF}xF}nGpJQn>MEPSS S6"<<<<N0{FCFB3D2A-A0FA-1068-A738-08002B3371B5}P j<,@jPD<@jHD@ %,` T i 0%j`4@j8$@j(@4@jLL@ P8`(P8`(P8`(P8`(   A8@0(  A8@0  A8@8  A8@P@  A8@H  A8@P    @`  p  @p X@$  @  X@ @ HX@,  @  X@ @  X@4  @   X@ @ X@H <  @ @  X@ @ X@ D  @  ` h@ @  @ x @@ LH x ( @ 8x\X$ ~P$*\Rffff*1450813232P    (08 B @84H x] 8] `] ] ] (] P]  & !  !  !  !  !  !  !'i0( ``Attribute VB_Name = "PedigreeItem" Bas0{FCFB3D2A-A0FA-1068-A738-08002B3371B5} z@GlobalSpacFalse bCreatablPredeclaIdA@ExposeTemplateDeriv$Cus tomiz COp tion .licit Pub FamilyFAs Long Individ@ualID F ather Mo Gender" AffecJStatus LiabilityClLas[un PXT h~P*\R1*#21b$*\Rffff*1550813232L  (H`x "  $PP"r VT0JHJ`x x] (蝄____] P蝄___] ____] x___] (_____̞] P _____엖H z z! %'* *$.. H!JG B!J.j z$!0!' z$! '" z$!2' z$!4'ox ``Attribute VB_Name = "selectInfo"" Bas0{FCFB3D2A-A0FA-1068-A738-08002B33 71B5} zGlobalSpacFalse bCreatablPredecl2aIdAExposeTemplateDeriv$Customiz COption .lici@t Pub rowNo As Long ' ____col$Start&__ "srcStriF__̞Chee0Works' F5Sub` getS(pSourl9) ODrro@r ResuNext"= VBA.Left0, InF"!@") - 1S&(= Bs(CIf Err.Number <> 0 Then LAppfaAl.Actz&Cm= RangeD#).Rows.Coun1Cm  /~f @Column End Sub rU 8a@L٧)   / i     7 q     9 0   4 8 < @ D__SRP_c__SRP_d2statusBarControler& FSNPLOHA1H   ZarU X(1 `Q0 @4 @$8@,<@4@@<D @DHn  kQx      !"#$%&'()*+,-./012345679:;=>?@ACDEFGHIJKLMNOPQRSTUVWXYZ[\]^_`abcdfghijklmnopqrstuvwxyz{|}~(PP% ~P t $( 08@H` Bhp xB B B B " " "  " (08" @HP $X   "   " 8 P $h   "      6( `  0   2 0 H 4`   2` < h ,--k"N$_TOFOn*=h8+3ql;CHڙjGxME PSS S<<<<<N0{FCFB3D2A-A0FA-1068-A738-08002B3371B5} b<@bD@ ,` i ,8`  i ,`x$i ,`(i ,X`8,i `0i `4i x`X8i `<"i  8 `@ &&%i   `xD Kiiix i i   `@XH R) x %, `L Yi   `@P ],`@` Ta)  %i  ,0`@ Xd)  %i  ,$`@p \gi  ,`<1  6kgϸ[dO z _*=h8+3q Ax١~ xME PSS S<<<<<N0{FCFB3D2A-A0FA-1068-A738-08002B3371B5}%  %8S % `@ )j %)n % h`@ i0)jPX %)n x %`%"4@"88@@`hpx@@@ h @ ` X0 ``H(08H80  `8(` ( @ @ x(  p @8~P,   @H " PX`h ,p , ,  "   &    " ( 0 .@ 08 H " P X` hx 4 T  xx 2005.Jan.11__̞Chen Bowang in DKFZ]@]@@ j' n'  n!l9l. n!9 n!p9p99fqHo@] clear and init Progress.Visible = False n9fq j !p9p99fqxdp n(f   n!9 d$%9P9fqkA@o .BorderStyle = 0 .BorderStyle = 0' .BackColor = RGB(0, 0, 255)8xAttribute VB_Name = "statusBarControler"" Bas0{FCFB3D2A-A0FA-1068-A738-08002B33 71B5} zGlobalSpacHFalse bCreatablPredecl2aIdAExposeTemplateDerivCustomiz COption .licit '2005.Jan.11 'Chen Bowang in DKFZ P15 myPercent As Label rogr es Pub!3 Sub'it"( , p) 7=  =IWith*Â.Top@ZALeftHeigh Wid@= 0aVisi #End ) @GYaGJsetSELageUSingle,CFZQDim0 str@ng9&If, T~'clear ra'inA+P\.3]HW@ N 'A.BorderStyNIE ack Color8RG B(0, @255If 8KH. 9}.9 #jEEIRTruef(bK+"9*'bkCaÀ= RoundL* 10a') & "<%"k`GIfDoEvs\@ `ji  ,`@0 dmi  xP%b4@b8@b(@@xxX8 (08%` xxX8 (08p xxX8 (08 xxX8 (08 H`  `  ` ``hX HXHX@ @ P08@@ @ @ @ @ @ @ @ @ ( 0`x  ( P x  ( p@ `  0X(H8  H 8h   HxP   " 08@HPX`" h "p "   "B@  "  0 B 8(@ XB `$h B B B  Chen Bowang, DKFZ, 16.Mar.2005P]@]@]@]@call]@(x 'i 'ih8 'iP 'i8 'i X 'o 'o 'ox 'o 'oPublic Property Get getSNPid() getSNPid = SNPid End PropertyPublic Property Get getCH() getCH = Ch End PropertyPublic Property Get getLoc() getLoc = Loc End PropertyPublic Property Get getGeno() getGeno = Geno End PropertyPublic Property Get getLOH() getLOH = LOH End Property0Public Property Set setSNPid(newSNPid As String) SNPid = newSNPid End Property*Public Property Set setCH(newCH As String) Ch = newCH End Property,Public Property Set setLoc(newLoc As String) Loc = newLoc End Property.Public Property Set setGeno(newGeno As String) Geno = newGeno End Property,Public Property Set setLOH(newLoc As String) LOH = newLoc End Property8 ' ' ' ' 'o !' !' !' !' !'o8 , , , , 'i[ o   %'i  %'ix0  %$'$iP  %'i(  %'ix(Attribute VB_Name = "SNP LOH" Basp0{FCFB3D2A-A0FA-1068-A738-08002B3371B5} zGlobal!SpacFalse CreatablPre declaIdAExposeTemplat@eDeriv$Customiz C'Chen Bowang, DKFZ, 16.Mar.2005 Option >licit P 04 ID AHs Sng C"h Loc Lo!Geno 'pcall"҂ ingle FuDncCgetS.@%EocA+Ub !? " !0C_ @Y v0D-Fv,#u' @!tkA!j@ q f1**?B gxbssFrom$)=.EydCH  u OSW 1E Fi&[pY& "," & Q q3 2j ynt ) Debug.RN b& = Equa>ls7 "#Booleanr ()) _P` okqc`2(] IsHomoO sP_f.=Gv qcxNoC@Is^peter H frmOR dT9Standard_IRN__SRP_10<#8__SRP_11<U " $ @  P` 0h 0x 0  " (  d ( 08 (@ (h ( "      ( 0 0H X ` h px  " " 8 N    F( p $ ^ , 8 $P " x xgG//kuy@߉My3_3LȸMlЫdPzbNQvAsIcxjxME @SPSSS<<<$<=2 on the same chromosomeusage:1. run the macro LOHstretch()X2. select the data area includeing 5 columns: SNP_ID, Ch, Loction, call(genotype)and LOH&3. tell the macro where to put result. 4. click RUNBowang Chen, DKFZ, 16.03.2005]x]]]@X]p]Ph]] z B@ ~ B@ !''  5 5 A@h +@5  5 5%5  5 5% %5  5 5% %5  5 5%$ $B@ $!& $' $!& $' qX  @  `      !  ! A@h $!&' $!(CASE $!AA $ +d@ $ +kd $!AA $ +d $ +kk         A@h $ $ $ $ "B@  "! "! "! '  "! "! "! '  $ '  $ '  $ '  $ '       "B@ OR55 5,95%CIL55 5,95%CIU55 5,X255 5, "!*5 5 5,5 5 5,5 5 5,5 5 5,OR_MH5 5 5,95%CIL5 5 5,95%CIU5 5 5,X2_MH5 5 5,  5 5 5,5 5 5,5 5 5,5 5 5,q With targetSelect .srcSheet.Selectx .srcSheet.Range(.srcSheet.Cells(.rowStart, .colStart), .srcSheet.Cells(.rowStart + j - 2, .colStart + 3)).Select Selection.Copy End Witho  !5  5 5, !5  5 5, !5  5 5,Q .srcSheet.Cells(.rowStart + j, .colStart + 3) = snp2.getLoc - snp1.getLoc  ' !5  5 5, !5  5 5, !5  5 5, ! ! 5  5 5,  'qox/Attribute VB_Name = "frmOR" Basl0{470FA1F1-8810-CE42-9D5E-5A6E385129D2}{34DC2865-207A-244A-AEB9-942204D3E} GlobalSpacAnFalse CreatablPredeclaIdTru @Expose]Template DerivCu@stomizBO@ption .licit P!% Sub UserForm_Initiali@ze() Orror ResuNext ' Me.Ca*SNP too ls: "Image1.Visi setStatusBar 0 With Percent1.TopIpropgresA AL8eftHe8igh Wizd="M-End A) MKPCommandButton1_C@YkPBJ2.EnAfF"?Me%MousePointer8fm HourGlass OR_MH Sce:=RefEdit1, @TargetF2$DefaulbclIHid,G'w @G1 G'#d'72I)(JR As Single[Dim str@ng$IfEQA C Then 0'cleV< idf)PS]a$a;X&BorderSty"ce.ab h.BackCol`x= RGB(0, @255C abi fU1jEB>AN(0 BaP2%hF* ) "Round!M* 10.) & "%C(?k"If DoEvs''This macro finds theaZetch wLOH>=2 Bchromosome 'us\: '1. run `c!2. select"d ؂a@acludej 5 column_ID, Ch, Loc, call(genotype)h@ '3. tell(where put _H. '4. cqU RUN 'B owangen, DKFZ, 16.03.2005 nQ(Q>/QC&QAiALong, jkcCrcScENewDInfo, tWct6mySa}0wA s"7inAgje,xfaD()1DouPw, bcd'JabccddphMaklHaenszelS19S2<rsU.kSheenK3oBReWrowNokpPVj12BC6"@ i To .qR - a>:Li / (G&Q i).D5.i.C1sr@rt + i, .60), _=VBA.UCe(/ow/1n)??to m 2? Val  ) 3)a0= Max(#@224ine! iY%a(m mr8Bsb/scpGd|)f+O*KB*11ODise'`2"CASE"oҔ?=2Sy_MH,{@L ,|}f03P@S1 / S2||L_>$sLI>End }'}Ok0Range(rt) *@j - >3)).-ion.Cpopy "FSub Private ` outputLOHstretch(Snp1 As SNP, snp2ɡsInfo, ByRef jLongc/(' (L@.aNPiʱLCH<_JMELocC,O+`;1jj`!14&e 9?&rt"&?&Q"&E!&%&&93H~/ }JKxME(6 << <PH+.`@i0`i2+4`@i0i2+8`@@i0`i2+:`@ i0i2+<`@@ i0`i2,%(`(  @``(  `(  @` (((( X0~P$*\Rffff*1650813232B  B ((40XB `.:hB (4B .:  x 0 2'.iX\(\? 0$6  2'4i \(\? 0 $6  2'8li`{Gz? 0$6  2':i({Gz? 0 $6  2'<ixİAttribute VB_Name = "Standard_IR" Option Explici t Pub Func`SIR(O As Sin@gle, e)9 VO / e EndT_CI95L)Z1`(0.98 - Sqr(O)) ^ 2'rU.9 U9+9 + 1%,;9t9L;1.2t9t9B:`: rU~| ZZ ZAZiZ5rU ,` **,` **,` **, ` **,1` **nrU~|  9!S 6-- ------L$ i$idk(, 0   OddsRatiosB__SRP_12"0B__SRP_13eRiskRatios$<$0 $P`h B  p$x B  $ B  $ (B  0$8 XhB  p$x B  $  B  $ (B  08XB  `$h B  $  B  $  B  @$H hx 8B  06,n08B  @06Hx,n B  (dB  (d0B  8(d@hB  p(dxB  ..u;G>kYxMEP"$> <<< <<<`,% %+*`Pk`  ii ii+@`J   i@i `ii+B``Jii i @i+F `Jiii i+J`J` iii i+N`J $i@i`i i+R``J(ii i @i+T `J,iii i+X`J`1iii i+\ `J  5i@i`i i+^` `J 8ii i @i+b `J <iii  i+f `J`  Ai i i  i+j `J  Gi@ i` i  i+n` `J Mi i  i@ i+t `J Ti i  i i+v `J` \i i i  i+z `J _i@ i` i  i+|``J bii i @i+~ `Jeiii( i+`J`hiii i+`J ki@i`i i"@ `   `  ` `` >x `   `  ` `` `   `  ` `` `   `  ` `` `H0`* @ "@ *`*x *@ *  @*`*(* *`*(* `*`*(* @`*`*(*  @*`*(* *`*(* `*`*(* @`*H* @*`*(*  *`*(* `  *`*(* @ ` ! *` *(* @ !!("!* "*  *X @ @ @ @# @##X#* h#* ` *X @ @ @ $` $$$*$*p @ ` *X @ @ @ @ ` %%0&&* &*p  *X @ @ @ H'  @H''`'*p'*p*X @ @ @ (((*(*p`*X @ @ @ )`) *****p @`*X @ @ @ `**p+h X@ @ @  0** @`**** X#~P$*\Rffff*1850813232$*\Rffff*1750813232o B 06HP$X $xB  . 06 ((dB  (d  x]    '*d(     "B@ "!*'*xkpih'this will return the OR of minor alleleBowang, 21 Nov 2007    '@d     "B@ "!@'@ki     "B@ "!D'BiP`     "B@ "!H'Fi      "B@ "!L'Ji     "B@ "!P'Ni     "B@ "%R'RiP`     "B@ "%V'Ti      "B@ "!Z'Xi    $X'\i     "B@ "!`'^i``     "B@ "!d'bi      "B@ "!h'fiJune 15, 2007, for Barbara     "B@ "!l'ji1'July 06, 2007, for OR and p-value of copy number    'nd    $R B!p%r'nki`    'tdx    $T B!p%r'tk@i8    $X B!p%x'vi    $X B!p%x'zi    $^ B!p%x'|i`    $b B!p%x'~iX     $f B!p%x'i     $j B!p%x'iH````0````x`V`0 `W ` ` `{ ` `8`P``n````eHeh(hAttribute VB_Name = "OddsRatios" Opn Explicit Dim MH As New MantelHaenszel PubP Funcp$(ahDo>e,T b c d )! Varie !If a0 OrA= cdThen,0}""ElseMH.set@Data aJ, c, dEnd If v ~R_minor}'this will return the OR of 0 allele 'Bowang, 21 Nov 2007V.3NMDMMCI95LMCTxOR_@8 ^s@ 9% @՝C%$9LF%9La%5USJ5Ug%UI99䁭~?8{d%9X2%C_3І@X2$B()$X2MHV{`=< oPowerKǣ %b95K&@# 79%_] %9%#7o x8{/h_  &R? `e OB_ b(}999KK ^ 'June 15t t, for Barbara  / / _)/ / 9 ? O P ly 06Y Pap-valuecopy number 6 ߰ #b0 pO &Ap!an.Worksheet.ChiDist(@!_<, 1)RnPY//RB[/#OODq o on pa lཿsbU8NormS5EzYY{ 95? ? ? sD: 95_ _ _ g_ _ =_ _ _ _ _ _ \ E(')  9  AX/-"0U 9 d   Ze) As Dou ble OR_Power9 = Application.WorksheetFuncDNormSDist( nK(a, b, c, d)) End d 0   0 `  0    0   0   0 `  0    0   0   0 `  0    0    0    0 `   0    0    0    0 `  0    0   ' 1'  $vi$v`$v $vi $v $v`A $v  $v  $v i$v` $v $v i'    '` $v $v $v i$v`$v $vZrU 8`++++8`++++8q` ++++81` ++++8` ++++8` ++++81 ` ++++8 ` ++++8 ` ++++8i  ` ++++8 ` ++++81 ` ++++8 ` ++++8 ` ++++81`++++8`++++8I` ++++8` ++++8` ++++81` ++++8` ++++8` ++++n   '   '    $' $'       $6' \(\?  ' $'iH]`x]] 8   '   '    $' $'       $6' \(\?  ' $'i0P](@X]p]0   '   '   '   '   '   '   '   '   '   '   '   '   '              'iH] 8P'th]h t]Bo   '00   '    $'  $'@       $6' \(\?   ' iphxAttribute VB_Name = "RiskRatios" Opn Explicit Pub Func`V(a As Long, b*cd)Si@ngle If aw0 Or:= cdThen,0tqElsK * (b + d)X) / ac)):nd If EjrR_CI95L8rDim RR|, LnSE9L %m1 m0:n n taEԊcJdH@=j+ c>0@_V4= È@, c,^7=g(RRC_== Sqr(1hfb - @0C E@P.96 * "Wl(( )yUyYMu @H..PB  88FHB  0P8F`B  8HXhxJN(x B 8F($&` x    'd0        'kxip] = ]( / ]@Xp32*\R0*#15*\R0*#14 (HXp  "     0 @"P06p 0@P "` f@T(2:8p  ( (6V  0@P`p#,$:$=x?kcHD3O2(*=h8+3q'Fnx'FnHD3O2(MESS S>"<(<<<<,<0<4<8<<<N0{FCFB3D2A-A0FA-1068-A738-08002B3371B5}8 j D,@bP@b @>b @b  @j2 T< @j2 dL @j@t\@j*H |d@jDp t@jH@jP @j` @jh0@jl @jV@ %*DL ``k77ii i @i,T`(+Mi ,B8`kPi @`,J`kxUi `,F(`kZi `,N`kh_i `,R`+ di ```` ````,\ `+qi ,^`+`ti ,b `+ wi ,f@ `+  zi ,j `+ i ,n `J ((i (  %jX 4@j<$@j(L4@bx@b@j\D @jlT @j@hl@jL|@jZ@jd@jX@H h( @p  x X 0 X `  8 P(0@0 8 $H h( @p  x X 0 X `  8 P(0@H h( @p  x X 0 X `  8 P(0@H h( @p  x X 0 X `  8 P(0@8X@xd8  @0x0x@x 00@( A8@80 A8@80HPZ`dhV2@ @ @ @H 8@ @62BJ@ `FN\^bfjlRTVx xhB`B`x`hJ`Jhh hF`FpphN`Nxxxh\`\h^`^xhb`bhf`fhj`jx0H`hR`RhT`Tj22X@p @$8   !8@@,8   !8@4  @ D x@xXX ( @ 4WT@  0 X  >@~P$*\Rffff*18508132 B$8 B&( 8B@H&Pp B& B& B @$`$x$$JN PBX$2` B$2 B$2 B$2 0 8BX$2` B 0\  8 Z 2h   P  ( \@ 2   T ` p  \ T H ^` V  ^0 X  ` Z`  ` \8  b ^ x  x] 0 X  I95]@(P xle]@ ]  ]  ] @] H ] h] p ] ] ]  ] ]  ] ] 0]  ] XPublic OR_P As Double  (  (  (  (     '    '*'D'L'H'P'Z'`'d'h''V'2''k   '   '   '   '    '*` OR_minor = IIf((a + c) <= (b + d), OddsRatio, 1 / OddsRatio) 'consider both case and control   * *$'@5consider only in control *$'       '2 2$6'   '   2'   '2        '2 %B'Dad %J'Ls: %F'H %N'P %\'Z %^'` %b'd %f'h %j'l %R' %T'VHo@`  2   2  2'Ti]  \(\?  ' $'Bi8] \(\?  ' $'Jix] S㥛@  ' $'Fi0(] S㥛@  ' $'Ni]0H]`x   '   '   '   '   '   '   '   '              'Ri \(\?   '\ip  S㥛@   '^i8 S @   'bi /$@   'fiJune 15, 2007, for Barbara@ z6@   'jip$R B!p%r'n=ChiDist(X2, 1)i01'July 06, 2007, for OR and p-value of copy numberSPublic Function OR_P(a As Double, b As Double, c As Double, d As Double) As Variant, If a = 0 Or b = 0 Or c = 0 Or d = 0 Then OR_P = "" ElseJ OR_P = Application.WorksheetFunction.ChiDist(OR_X2(a, b, c, d), 1) End If End FunctionUPublic Function OR_PMH(a As Double, b As Double, c As Double, d As Double) As Variant, If a = 0 Or b = 0 Or c = 0 Or d = 0 Then OR_PMH = "" ElseN OR_PMH = Application.WorksheetFunction.ChiDist(OR_X2MH(a, b, c, d), 1) End If End FunctionVPublic Function OR_Power(a As Double, b As Double, c As Double, d As Double) As DoubleM OR_Power = Application.WorksheetFunction.NormSDist(OR_PowerK(a, b, c, d)) End FunctionXPublic Function OR_Power95(a As Double, b As Double, c As Double, d As Double) As DoubleO OR_Power95 = Application.WorksheetFunction.NormSDist(OR_PowerK(a, b, c, d)) End FunctionXPublic Function OR_Power99(a As Double, b As Double, c As Double, d As Double) As DoubleQ OR_Power99 = Application.WorksheetFunction.NormSDist(OR_Power99K(a, b, c, d)) End FunctionYPublic Function OR_Power999(a As Double, b As Double, c As Double, d As Double) As DoubleS OR_Power999 = Application.WorksheetFunction.NormSDist(OR_Power999K(a, b, c, d)) End FunctionZPublic Function OR_Power9999(a As Double, b As Double, c As Double, d As Double) As DoubleU OR_Power9999 = Application.WorksheetFunction.NormSDist(OR_Power9999K(a, b, c, d)) End Function[Public Function OR_Power99999(a As Double, b As Double, c As Double, d As Double) As DoubleW OR_Power99999 = Application.WorksheetFunction.NormSDist(OR_Power99999K(a, b, c, d)) End Function`````0```suom `xboih`ecca,`ecca `ecca ` ` `H8Ph0 Attribute VB_Name = "MantelHaens zel" Bas0{FCFB3D2A-A0FA-1068-A738-08002B3371B5} zGlobal!SpacFalse bCreatablPre declaIdAExposeTemplat@eDerivCustomiz COption .licit Pub a As Doe, b c d P=A m1m0n n LnOR SEPv :N e v2OOddsRaCR_minorAOCI95LU9S 9P Pow`er95KC9/WXKX2MH%'OR_P_Sub s(etD@() B Me.aaUbbcc+dNa b+W+ cIf[= 0 Or !"0 ThenBA'CC?-U@0i>l`=)<1/6i6 v v12GoTo outEnd IfB}=`)+0b,@}4`}=0")+ C* d) / (c *` b) '/eo=` IIf( ) <= (B ),b , 1) 'conside=oth cἆatrolc5 cA d only in b= Log( !.!R!SS= Sqr(vb_!4b#c@NC4 7* '̀3* `0/ 3`0@ -Na(N - 1)mE\`o {(aA]'U'B^&9L(j9eH`$\9K/9?O9Wr5SX25UMHp2: 2OFuFuncvyA()R..- e)/ v?EUI4\Dim ugw@+w0 .96p( W $(6) ic `  o #"4+ 1 R_A1 U )  99t2.576/I'C  90  / ( Cf4? ?9- a.DG0c, diA(aEcd'=a MbE LJ0R@aO@hP !i- aE2bDub Pb j- c0 = d^d@p*/o`kD jd`"/`q/ PAe<_B0 (Abs(+) 2tT<{:%VRQ;'N W'!B@3.291F7?123.(893RKO 'June 15, 2007, fBarbara?"e4.4172 =Po#AppHQn.Worksheet.ChiDist(0!A EX2Y006a@p-value ofpy number oµtVariN@ant ' If a = 0 POr b@c@da ThenOHR_PX""$Else8Application.Workshee tFunc"Ch@iDist(IX2(a, b, c, d), 1)Und If 'E7 'Pu*bV  MH(a As DoeK c d B) VariM~HeowerPC`V8[0NormSszP KttqA 95- C?.`9?..90.99\9jgqE99Eic~//00^`)_S| aZ( Z Z aZ   Z  Z  aZ@  Z-__SRP_159frmPedPhasegSNPsample-#MHstrataA+(Q`+(`+( `+(Q `+( `+(  `+(Q `+@ 4@$ <@, D@4 LQ  @< T @D \ @L d @T l@\ t@d |@l !@t 9@| Q@ i@ @ @ @ @ @ !@ 1@ n4F$F$8H "P X "` "p "  " 2   $ &@ *h     .  ( 0 8@ `&" " " ( "08@ "H P` "h p "  "  "  ""&,(H "PX$`&p<( rU P9  SYZ]ia@٧)  9/i7q!?y7q!?y)G1O7q 1   !!!i i( i0i8" \6---- -----|-----------T-l-t  " |T -z|k||@ G,2t|*: - - - -TtT*   z\l(zlzlzTt(zzz\dVzzzzz\z\z\ -TiiiiiiiiiiimX$ xH8z4zdz4zdzT/H$ xH&z\(\?z */H$ xH&z\(\?z */H$ xH&zS㥛@z */H$ xH&zS㥛@z */H$ tD$zzz\$zzz\$zzz\$zzz\z4z<zDzLN/HD$ p@2z\(\?z z /@$ p@2zS㥛@z z /@$ p@2zS @z z /@$ p@2z/$@z z /@$ p@2zz6@z z /@$ 0   4 < D L T \ d l t |             i '  Z` a Z  Z8 Z       !"#$%&'()*,8./01234567+9;<=>?@BCDEFGHI:LMNOPQySmUVWXYZ[\]^_`abcdefghijklRnopqrstuvwxz{|~.xp1.WXkԪ>HAg?;0Aw1aNO$E)B:eE[U̮,CEZUBxME@SPSSS<< ` BDo `F `JrK H`NOR  ` Rs  `  Vor  `$ Z H `@( ^  `@, e `d@0 m`` h`T@4z`` `@8 `@<` ,h`@@ @CCiz`ii  ```* %  % X@@% ``DD<<```:` 8  pX``` h`@ H%i`  X %   %b 4 @bj8@"(Dx@"X |@b@HH0 Hhh X H  (PXXx HH0 Hhh X H  (HH0 Hhh X H  (HH0 Hhh X H  (()X)( @ P@&%8`h)(N) j )@j)( @ )p('`)p(')p(')p(')p('@)p(')p(X|)X|)@ @ @ )X|)@ @ @ P)0PN) @ @ @ @ p @ 8 @| l @h )d P8 )PhN) @ @  p@ H @ x @| l @h )pd @b \ @Z )T p(@)@)( @ ()`()|h) @ ( @@ (@ )( @ @ p( @`(0#) ) @ P hhP P  P %P   0  `      ! (!( @ @! P! " "  " @ @ ! @x 8"(h H#d "#T h"D @4 "$ @ " @ H# @  #0# ##pHP*#X @ @ @ #"#$##`)$* $ 8$+H$ `$+p$ $-$ $-$/$ $0) $0%6h%8x@%&)(&@  (&&&p &@ &( @ @ && '' @ )p )X| @x @t @p '''l ''h '(d ()` 0(@(!(# @ (X)() @`())) )`()))`))()0 )`)`(h( H*( @ @ (  @ 8) X X X 0 + ~P B 0P` .h " 0  ( $ 0H ""*6 (4D8p$x " 4F  2D(`$Rh $ "  "8 8  @P "X` hpx R v  $  <8  @ H B P X p    2 8 8 H X ` p  $.x 2 * 0 , 8 @  H ^X    ".  < X <h        8 8 X h  $.p 2 6 ,   ,.0`<< ( 8 PX `hp,jx   "  *( @P  Lh@$   $@(@H2Zh2P  &  0  @ :` "F >     8 "X D @ d >p x ( @ ` " @ , ` >x x 0 H hx "   &     0  0 8 @ HP "Xh 8p N   x] ] ]optionK(] (]0 ]X 'Dim statusBar As New statusBarControler Me.Convert.Enabled = TrueoH !t!d'j j$r.out+ A j$r .out.trans+lica !P(@Fuo 5P(@b, c, 5(@ En5N(@qHo@0, Me.Caption = "SNP tools: convert SNPHAP" d(f With Me.myPercent .Top = progressBar.Top .Left = progressBar.Left$ .Height = progressBar.Height .Width = 0 .Visible = False End WithA@h' statusBar.init Percent, progressBarA@A@A@PedPhase_work.txt'jPedPhase_work.out+PedPhase_work.out.trans+ PedPhase1+ PedPhase2+o Me.Convert.Enabled = TrueoH'o'o-b'ox-c'oXH-l'o8-m'o-i'o' !(@ !(@SNP data including pedigree !|(oH' !(@ !(@,SNP data including individual ID in 1st row! !|(o]] PedPhase.EXE   j'`  $'le Failure running PedPhase.exe. PInfoA@dh !N(@kPoH]8]P Convert_Click WinPedPhase $ $'  $'  Failure running SNPHAP.exe. PInfoA@ dx$$h$$h'D !N(@H ReadResult_Click'hkk B@oh$$A@ A@$$A@' B@ o] v9t  |!d$'atio, d@ |!d !d$' and ck 5(@ *kA@hnsider6 statusBar.setStatusBar 0, Percent, progressBar 9tqo zGj]2] j On Error GoTo 0  #pedigree and SNP data are separated1the original SNP from Affymetrix chip, all genome  B@ z B@]( $'  5" $sample 5" A@h  , Pedigree data $!5 5  5% $!k Pedigree data of ID 5 5  5% not found! ErrorA@' 5 (SNP (AA,AB,BB 5  5  5%$ dAT, GC, 5  5  5%$v k0 snp sampleqd1 the original data edited together with pedigree, one line one sample z B@  5 $sample 5 A@h pedigree and sex,affected ,etc5  5  5%  5" ( SNP genotypes (AA,AB,BB 5  5  5%$ dAT, GC, 5  5  5%$v k  sampleqk'plh H!J % P saveSNPDataA@'(Vih]]]@]x]$$' ': :G|j$ $'  !!minus the n of columu of pedigree$ Print #1, vbTab;  : samples name $ $' $ $' $     %'  _F  _M    markersSNP    :samples $  $' $   $' $    %| $   'the last 2 columns Print #1, vbTab; For i = 1 To nSample= at1 = InstrIndex(outputLines(i), vbTab, nSNP - 1)9 at2 = InstrIndex(outputLines(i), vbTab, nSNP)] tempStr = VBA.Chr(34) & VBA.MID(outputLines(i), at1 + 1, at2 - at1) & VBA.Chr(34)8 Print #1, vbTab & tempStr & vbTab & tempStr;q' Print #1, VBA.Chr(34) & VBA.MID(outputLines(i), at1, at2 - at1) & VBA.Chr(34) & vbTab & "_" & vbTab; Next i Print #1, "" Print #1, vbTab; For i = 1 To nSample9 at1 = InstrIndex(outputLines(i), vbTab, nSNP)% at2 = Len(outputLines(i))Y tempStr = VBA.Chr(34) & VBA.MID(outputLines(i), at1, at2 - at1) & VBA.Chr(34)8 Print #1, vbTab & tempStr & vbTab & tempStr;q' Print #1, VBA.Chr(34) & VBA.MID(outputLines(i), at1, at2 - at1) & VBA.Chr(34) & vbTab & "_" & vbTab; Next i Print #1, ""V`oX]@ clear and init Progress.Visible = False n9f9q j$@9 n!p9p999fqd n(f j  n!9 d$%9P9fq(k A@o* CommonDialog1.fileName = TextBox1.Text On Error GoTo out: CommonDialog1.ShowSave* TextBox1.Text = CommonDialog1.fileNamepxAttribute VB_Name = "frmPedPhase4" BH0{5CA3A31F-E5A1-DE4C-8BCD-C4EFC8B28BA8}{B74BC2C1-3EDF-C344J71-6AE7D34CC4AC} cGlobal!SpacFalse CreatablPre declaIdTru @Expose.TemplateDerivCustomizBOption .licit Dim allTogether As Bo@olean  fXile Sng $ 'o#+ out(1@ To 2),` sheeinSNPtypeInteger '(sta tusBaB.New Contr5@2r@9P@J@L Sub CommandButton2_CBk() ' onDi@alog1.?= TextBox,1. ORrr`or Go:=:ShowSav"eMe.%vert.EnfJ# End3 6_Change5A51 ]  C^)ParseF}n() & ".M "J x= \ .trans ?33UserForm_Activ 8$With Meb!*gE.,ReadResuli3g &C /InitGiz/Da N IANa#r\ t os: conAD @HAP#'Image1.Visi# !.myPer0centTop:progrese. Left A(HeighmWid`2= 0h\)psetS&xD&x.i) D, h?Cy1y78hd"eE_work.txtC0d3cao1 l2"FP)PRefEdit` E-nm)$n`Q⯿<2`Ia2%J /<@t8ypePA'AA,AB,BB26vbTab $_AB_Code(%iC)=E 'AT, 8GC,@-CGT?j+i)=`6K@wnpg\" ?Qj}W ! & ' ʥedited tewہg&' one liLZ c@fd(M) 6 ;fsex,affp,etc*5g/*<!)DB77 ]1k6s 8np/8rF' 88iZo/88A8c   9/^b ?8tt=w;87?{ZTrucZY]HlerYeVBA.(P.Number)aOKOnlya?cB3a_cClxoses2UfSub rrange`mPhase=(5?nS⇁n++LD3{newHapp\at1wat2bB&Resu 5lRFs(3(1Ee= đ#09GGqE`xit S Q% VSplit;1bpiRe1M"- 6minusb^nPumu@"]2Be 2) G:2 9MJ0xs n`bQq=@ Instrex i, 1#2p/#(2'u!= 2Midnq+ Т!- ?|D5P_FRM"C?C!!^T2 'marker]3aj6Sleb1t7xjW,O Replace(s`Pt` "|.X sNjcBlast 22 0ns^ #1, vbT@ab; ' For i = 1 To nSampletat1|InstrIndex(outputLines(i),xNP - 1) |2&| :tempStr>VBA.Chr(@34) &  MLID+ a|t2-;LPprint,8&L, J3ʀ"_"Next i^>"" vLenbqWKA bPpTpFpA2Close@ : End Sub vate setStatusBar(Percentage As Sin gle) ADim tgBIf H= 0 Then 'cl ear a init+Progress.VisiblepFalse With ~p BorderSty 0& b CackCol= RGB(0, @255c aHeight(. Wid" T U#E&Tru*rEkA?*)0.C@aption RoundF* 10&"%"+FIfDoE vQsW B B " " " "  "  (08@H" P "X "h x "B2j  " Chen Bowang, DKFZ, 27.OCT.2005P]@X]@]@call]@` 'i '(ip  '&iX 'i@ 'o(@ 'o 'o 'o` ' ' ' 'o  !' !(' !&' !'o` , , , 'S @i[ o<ekق.=J+Y*=h8+3qʃ}"CDE xME PSS S<<<<<N0{FCFB3D2A-A0FA-1068-A738-08002B3371B5}XHb<@P%,`i ,( `  i ,&``$i ,`(i S @ @` ,i `0i `4i  ``@8i  `<$iii   i'Ls:  `@`@ *)'h %, `D 0i 2  `@H 4P(%b4@b8@ b@@(`X` @ hp`X` @ `X` @ `X` @ h ` `  (  `   0  `    X @`@(&( @ @ @ @ H@ 0@ @ (|  `X((((~P7 $( 08@X B`h pBx xAttribute VB_Name = "SNPsample"  Bas|0{FCFB3D2A-A0FA-1068-A738-08002B3371B5} zGlobalSpacAFalse bCreatablPredeclaIdAExpHoseTeateDeriv$Customiz C'Chen Bowang, DKFZ, 27.OCT.2005 Option >licit P04  As$ Sng Di se Geno 'callAge ingle Func>Hget6()   En|d D'Q.= DW+D+"0= @WG@@0  Sub bs Anew:C)D= @ED8(MMA+AMH BQC0 F ub DCDB,>PbK !(v(< B"/b !Ba "FPpFromoŕ:.)` FF*g!kInFt[S")t & ","o Jy 'ntAc$Debug:. "b.0 2 2 2  2@$<`$6$6$6$66(H Xx](](P]Pxx@c]]@h] @h] 0] X] ] ] ] ]'''' '''''2'''' ''2  " "  $"! '  $"! '  $"! '  $"! '  $"! '     8if the stratum is too small, we add it into next stratumdp     '     '               '      '   '   '   '   ' 2    '2 2         '2   '   '   '   '  to clear current temp stratum'''''kp   '` `$'   $6' \(\?  $'D \(\?  $'L S㥛@  $'H S㥛@  $'P  2   2  2' \(\?   'Z S㥛@   '` S @   'd /$@   'h N)     B@ 1 / dox`0P@`Attribute VB_Name = "MHstrata" Basx0{FCFB3D2A-A0FA-1068-A738-08002B3371B5} zGlobalSpac False bCrewblPre declaIdAExposeTemplat@eDeriv$Customiza COption .licit Dim S1 As Dou, S2s34LnOR SEIaa bbccddm MTm0 n nv_K IIe N  PJic OR_MHCI95L U XV5@ 9M 9H Power95KK9WCrude6New MantelHaen`szel D@S@ub Conuctor(MH()' ) iLongB= 0@aɄ FcFAɣm#N[`[E[F4fv& For iLBound@) Txo UAa + i).abbbZccdd+NNIfB " Or a 0b"B" Then'if the um is too small, we a.it into next%EaA e++* d * gab.+* cC1+ (bc` / N)1,*(dCL%s9* r=+ /=+ /80 "<<N0{FCFB3D2A-A0FA-1068-A738-08002B3371B5}h h b (@bP@bP@bx@b  @b @b @b2@@b@b@b2 @b@(@jDh<$@j0L4@jHT<@jZdL@jdt\@jh|d@% % `8 kHx@@)"@ h %`%b@b@s b(@bx@b@b @b @bh@b@j`4@jLD,@jPX\D@j`lT@*l@xXxP0((Ph@h@HxXxP0((Ph@h@xXxP0((Ph@h@XxXxP0((Ph@h@P X X@ `    2 2@   H H  @ @ `6 0 DLHPZ`0 dh  <|2~P$*\Rffff*1850813232$*\Rffff*1;50813232*\R0*#150P(8 X&x "  (08@HPX`hpx222220F >H 2 2 b 28 X h x  2 <`    ( $8 ` h p x  __SRP_1a( S __SRP_1bOddsRatioStrata TM__SRP_18)4rU 9 YZ] a@0٧)  /i7q!?y7q5--------- -(-----  dd2{iz2{i$z2{i,z2{i4z2{iDz((Fz--z--z--z--VR2zzzz(2zzzz(zzzz(zzz( -z -z -z -z2zzzz(zzzzzzzz2z zzz( `zzzzzz(z(z( -zzzzzzzz-----(zzz4t4*0zzz*2z\(\?z*<2z\(\?z*D2zS㥛@z*T2zS㥛@z*\<zz zz zL6z\(\?zzd6zS㥛@zzl6zS @zzt6z/$@zz|6|||||im$ 4 < D L T \ d l t |+ qZrU <,`ys  @ 4!@$ <9@, D!@4 LQ@< Ti@D \@L d@T l@\ t@d | @l nrU~| &      ٥yQ)   i ) f*\R1*#14d P` " hpx L>*P h px4.   T  60hFNN( @"H"p""   * ( *0 P Xhx  B N B  T B   T XVx B   T LTX pB  R B  R (1,2qCFk& xME  " ""$8L> <0<<<L<4<8<<<Pp.%@ %`&+%@YEX%D x`pk++ii i p`^`  8: *h "^T $0````X +& `h k2) %i i +*`J`6) %+,`J:) %+.X`J0@)P %+0`JF) %+2(`JJ)  %+4`JhN) %+6`JR) %+8 `J8 V)X` %i i +:H `J Z) %i (i +< `J `) %+> `J e) %+@ `JX j)x %+B`Jo) %+DP `J( t)H  %+F `J x)  %+H `J |)  %+J`J` )  % @ 8@"p@(P   Xx HH (P   Xx H(P   Xx H(P   Xx H h @  @8 @P @ @ @p@ @ P(@0`h"` % @ @  @  @ @H @ @x @ @ @p %@-`- - @ @ @  -X @ @ @ `- 0- @ @ @ x 0-X @ @ @ 0xx(- - @ @ @ @ -X @ @ @ @@X- h- @ @ @  -X @ @ @  - 0h- @ @ @  h-X @ @ @ h- - @ @ @  -X @ @ @ H- 8- @ @ @ ` 8-X @ @ @ `8``x-- @ @ @ ( -( @ (0- -p-X @ @ @ H H ` -hp  -0 @ @ @ ! B- @ @ @ -( @ @ X"X"#p"-h" -0 @ @ @  # B- @ X@ @ -( @ @ h$Xh$%$-h$ -0 @ @ @ 0% B- @ @ @ -( @ @ x&x&&&-&( -p-X @ @ @ ( ''x('- ' - @ @ @ ( -X @ @ @ ))@*)- ) - @ @ @ X* -X @ @ @ X+X+,p+- +` - @ @ @  , ` ,-X @ @ @ ` - --@-@---h X@ @ @ - , X @ @ @ @- " ~P$*\Rffff*1;50813232$*\Rffff*1150812abd$*\Rffff*1850813232*\R1*#142$*\Rffff*1:50813232*\R0*#10*\R0*#B  R B  R  0@B  HNP hxB   t D &H(fpB   TfB    V f0 P B  X ` Tx f  B   X  B   R  0 B  8 R@  P ` B  h Rp   B  R    x] ] ArangeInfo is advanced than selectInfo, with worksheet information] ] ]8]P ](@tio E .getSheetInfo abcd 'abcd is an Excel address of lines of cell  C@$)abcd is an Excel address of lines of cell 5" .k5 "p 5 NDec 18, 2007 Bowang/DKFZ, to fulfil the strata OR for Haploview count oputput,like "586:1318, 524:1352"0we need to split the string to obtain 4 numbers.5  55%' ,$' $ :$'"$ :$'$$"$'$"$'$$$'$$$'d5  5 5%'5  5 5%'5  5 5%'5  5 5%'k         $"B@d     $"B@k  " B@qxopx !(  A@ !`'&i8  !(A@ !`'*iNDec 18, 2007 Bowang/DKFZ, to fulfil the strata OR for Haploview count oputput,like "586:1318, 524:1352" !(A@ !`',iXNDec 20, 2007 Bowang/DKFZ, to fulfil the strata OR for Haploview count oputput,Eforce to use the output of Haploview without the minor allele reverse !(A@ !`'.ixX !(A@ !D'0iH !(A@ !L'2i( !(A@ !H'4i !(A@ !P'6i !(  A@ !'8in setData abcd.Address 'we don't update the object if we call external function Strata_OR_X2(abcd As range),>other wise we use internal variable Strata.X2 in the next line Bowang Chen, Oct 18, 2007 DKFZ   $8 B!p%r':i`H Dec, 18, 2007 !(A@ ! B!p%r'<i Dec, 18, 2007 !(A@ ! B!p%r'>i Dec, 18, 2007 !(A@ ! B!p%r'@iH setData abcd.Address $D B!p%x'Bi !(A@ !Z'DiP !(A@ !`'Fi !(A@ !d'Hih !(A@ !h'Ji80````0``P```p` ` ` ` ` ````` `0@PVY   u   sv 89@xhPhAttribute VB_Name = "OddsRatioStrata" Op0n Explicit Dim p As Ne`w MHsX4srcSelect:rangeInfo 'is advanced than s3&, with worksheeHt i;rmn!aMH()zantelHaenszel PrivaSubStD(abcd0ing, al isMinor Boolean Haplovipt) iLongalllcg7io]Dc0aseA onptrol 50Double, b c {W '3.getSA[jL'BjAcel@ldress of linelBEetch,  If Nosbnd .colNo < 4 ThenFA SoW@}h| GoTo outE@IfRev 0 .row- 1}Fi@ F@.iH-)'Dec 18, 2007 Bow/DKFZ, to fulfile ` OR fBcount oput,like "586:1"3524@52" we neAqo s|t'@obtain-numbers..1J_= .ALI.C ells((Start0 + i,B8*aad+ S( , ","hCm0) :1k1aVal(hv0)b1c*} d2m Else2@_1olF30hHeE:h2 h3k|At$c > dO!i).se b`, d, c*.R0+a`+kNex&.Con uctрMH `:B Sub`€ic Funcb_OR&RaionRrWsJr"xe^.Adb,vFR 6 *p.OR_p Q P ] _m{   Tru2{dv_  8/_ng/_h/_u/_ 'o^i^oss, AS OOo& 's 20pp]ap '0rceAkus`2qAVopbn$ pf xrevm"FaV+=/-n$$CI95L$ $/ ssRwAO5A_UaBe>5U^UJ49?s4V9L?t;9?OZR_X2+Zr/$Q-ZWRX2X2P 1ibeט4 @ϣ 'Ьdon'tP updtQ@bj1if c> @vermf~r)A2), 'o`roC`E Eivaria@  .{an| # ~C0 ƿQL4P)Ap c.We<.ChiDist(A`u6 Public Function Strata_OR_P_minor(abcd As Range)$Doe 'Dec, 18, 2007 PsetD| f.Address,` True< = Appa|.Worksheet.ChiDist(9.X2p) End_Haplovi|ewD˙h6mjFpalse5?4nkowe ^*NormS»A95K) . ʩ.@/P$& 90"9KM9K_C1:99fF #`#   it* i<_"ncv4i4@.i4d\  iDiL iiiiiFp, p6 pNp, p6 pNp, p6 p* * * * iDiL iiiii 2iD!iL" iii#i$i 2iD!iL" iii#i$i2iD!iL" iii#i$i2n"*%iJ*%izix cT6pxN hhhhi4 ? iXx$ 0    0   0   0 X  0        !#$%'()*+,-./0123456789:;<=>?@ABCDEFGHIJKLMNOPQRSTUVWXYZ[\]_`abcdefghijklmnopqrstuvxyz{|}~0 (  0   0   0   0 H  0   0   0   0   0 P   0    0     f fx9N ANINQNX N N( N N f I  f *NH !   NNN!NP N N DrU 0`  08`   =Y,` =Y, `__SRP_19 frmCommonStretch"]frmSTRshared[MfrmHapMart07=6PN =Y,` =Y,` =Y,!` =Y,` =Y, ` =Y8  `   =Y8  `   =Y,Q ` =Y,Y ` =Y, ` =Y,` =Y,` =Y,` =Y,` =Y,` =YnrU~| >   `h  ( b ` h ( "   ( " @ P (X "  "&    0 0( 08HP X &`p x 4 4  &   ^( R b H"P  X`dh @    "  0HXhx  $D$D,, B x>9LLk+3:%F;bD/@ ?M6}X ZfHtDBe@hM:c4xME@SPSSS<<(*p     >P @* H  P X  >P`      >P (  >0 p " 8d"d"`R0P6d`"d"`R ( 0 V8 " " 6 * 2H 2 V : 0P   < < (( (P x : > 0 40 0h 4 4   8( 4` : 8  ( 8 @ <`   : : :0 <p  ( $ &  BH ( * , $ @ &` > ( * ,  P p  , & ( X( F F B $X V F F  Bh $ $    "@ :h $ & (   @ X (p " $ T B@ B > ! R0! B! B! >" X" x" " " " " # "# 8# \X# # # # 2$ @$ X$ x$ $ $ $ .$ % (% H% h% x% % H% 6% 6(& 2`& & F& 6& 60' 2h' ' ' ' " '' ' ((  ( (( 0(8( @( 0X( h( p( x( (( ( "( "(( 8( N( ) ) )()0) @)xPrivate Declare Function FindWindow Lib "user32" Alias' "FindWindowA" (ByVal lpClassName As String, ByVal' lpWindowName As String) As LongDPrivate Declare Function GetWindowLong Lib "user32" Alias' "GetWindowLongA" (ByVal hWnd As Long, ByVal nIndex' As Long) As LongPrivate Declare Function SetWindowLong Lib "user32" Alias' "SetWindowLongA" (ByVal hWnd As Long, ByVal nIndex' As Long, ByVal dwNewLong As Long) As LongPrivate Declare Function SendMessage Lib "user32" Alias' "SendMessageA" (ByVal hWnd As Long, ByVal wMsg As Long,' ByVal wParam As Integer, ByVal lParam As Long) As LongXTPrivate Declare Function DrawMenuBar Lib "user32" (ByVal' hWnd As Long) As LongPrivate wHandle As Long!Private Sub OptionButton1_Click() TextBox1.Visible = TrueEnd Sub!Private Sub OptionButton2_Click() TextBox1.Visible = Falsee(2) +End Subat!Private Sub OptionButton3_Click() TextBox1.Visible = Falsed End Sub +xSNP tools: Common Stretch (P d(f 0A@h j n!l9l not n!9faul n!p9p99fq J( Po.to find the common stretch of several samples,eck -the start and end locations and their thengtho"Bowang Chen, DKFZ, Auguest 2004XThe input data contains 4 colums of data: SND,chromosome,location and comparison_result.Kthe comparison_result was done by comparing some samples on their SNP data,\the comparison_result can also be one attribute of one sample, such as IsHomo(), IsNoCall().@ v9t |!d !dA@9 CommonStretch1 Source:=RefEdit1, Target:=RefEdit2 9tA@hC@qXoP@ common stretch]]@X]p]]]0]Hh] z z! %'* ~ ~! %', *'$'* ,'$', *$.. ,$.. z$!0!'%蝄____ z$! '"(蝄___ z$!2'"____0 z$!4'%___0 ~$!2'$"____1 ~$!4'&%___1 *!t$' SNP ID $ & ;Ch $ & ;Location $ & ;Length $ & ;q'     A@h%read a SNP data from excel table line  -    %    %    %    %$B@$%$$%  $$B@.% RetainSNP0 'retain last common SNP  ' d$$B@.RetainSNP1 'retain rurrent SNP' kd  G  $ &$$  A@j$$B@* RetainSNP1 retain rurrent SNP' k(d   G  $ &$$  A@j' k   G  $ &$$  A@j  G  'j B@H $ & % $   & $$B@H Selection.Copyo  ! 2   ;1the start point ! 2   ; ! 2   ;  2   ;  ' ! 2   ;1 the end point ! 2   ; ! 2   ;  2   ;  '' qXoPOPublic Sub CommonStretch1(Source As String, Target As String) ' common stretch' Dim SNP As SNPLocation Dim i As Long, j As Long/ Dim k As Long, l As Long, CommonLen As Long$ Dim rowNo As Long, colNo As Long, Dim rowStart0 As Long, colStart0 As Long, Dim rowStart1 As Long, colStart1 As LongO Dim SNP(2) As String, CH(2) As String, Loc(2) As String, Comp(2) As Boolean4 Dim srcSheet As Worksheet, rstSheet As Worksheet* Dim srcStr As String, rstStr As String On Error Resume Next5 srcStr = VBA.Left(Source, InStr(Source, "!") - 1)5 rstStr = VBA.Left(Target, InStr(Target, "!") - 1)! Set srcSheet = Sheets(srcStr)! Set rstSheet = Sheets(rstStr)4 rowNo = Range(Source).Rows.Count '蝄____7 colNo = Range(Source).Count / rowNo '蝄___* rowStart0 = Range(Source).row '____0- colStart0 = Range(Source).Column '___0* rowStart1 = Range(Target).row '____1- colStart1 = Range(Target).Column '___1. CommonLen = Val(frmCommonStretch.TextBox1)' With rstSheet2 Cells(rowStart1, colStart1 + 0) = "SNP ID". Cells(rowStart1, colStart1 + 1) = "Ch"4 Cells(rowStart1, colStart1 + 2) = "Location"2 Cells(rowStart1, colStart1 + 3) = "Length" 'End With k = 1 For i = 0 To rowNo - 15 frmCommonStretch.setStatusBar i / (rowNo - 1)4 SNP(2) = Cells(rowStart0 + i, colStart0 + 0)3 CH(2) = Cells(rowStart0 + i, colStart0 + 1)4 Loc(2) = Cells(rowStart0 + i, colStart0 + 2)5 Comp(2) = Cells(rowStart0 + i, colStart0 + 3) If Comp(2) Then! If CH(1) = CH(2) Then If l > 0 Then' RetainSNP0; SNP(0) = SNP(2) 'retain last common SNP! CH(0) = CH(2)# Loc(0) = Loc(2)% Comp(0) = Comp(2) l = l + 1 Else' RetainSNP17 SNP(1) = SNP(2) 'retain rurrent SNP! CH(1) = CH(2)# Loc(1) = Loc(2)% Comp(1) = Comp(2) l = 1 End If Else& If l >= CommonLen Then 'ShowStretch" ' With rstSheetQ Cells(rowStart1 + k, colStart1 + 0) = SNP(1) 'the start point? Cells(rowStart1 + k, colStart1 + 1) = CH(1)@ Cells(rowStart1 + k, colStart1 + 2) = Loc(1); Cells(rowStart1 + k, colStart1 + 3) = l k = k + 1O Cells(rowStart1 + k, colStart1 + 0) = SNP(0) 'the end point? Cells(rowStart1 + k, colStart1 + 1) = CH(0)@ Cells(rowStart1 + k, colStart1 + 2) = Loc(0); Cells(rowStart1 + k, colStart1 + 3) = l k = k + 2 'End With l = 0 End If' RetainSNP13 SNP(1) = SNP(2) 'retain rurrent SNP CH(1) = CH(2) Loc(1) = Loc(2)! Comp(1) = Comp(2) l = 1 End If Else" If l >= CommonLen Then ' ShowStretch 'With rstSheetM Cells(rowStart1 + k, colStart1 + 0) = SNP(1) 'the start point; Cells(rowStart1 + k, colStart1 + 1) = CH(1)< Cells(rowStart1 + k, colStart1 + 2) = Loc(1)7 Cells(rowStart1 + k, colStart1 + 3) = l k = k + 1L Cells(rowStart1 + k, colStart1 + 0) = SNP(0) 'the end point; Cells(rowStart1 + k, colStart1 + 1) = CH(0)< Cells(rowStart1 + k, colStart1 + 2) = Loc(0)7 Cells(rowStart1 + k, colStart1 + 3) = l k = k + 2 'End With l = 0 End If l = 0 End If Next i If k > 1 Then k = k - 1 'rstSheet.SelectV Range(Cells(rowStart1, colStart1), Cells(rowStart1 + k - 1, colStart1 + 3)).Select' Selection.CopyEnd SubPrivate Sub RetainSNP0()+ SNP(0) = SNP(2) 'retain last common SNP CH(0) = CH(2) Loc(0) = Loc(2) Comp(0) = Comp(2) l = l + 1End SubPrivate Sub RetainSNP1()' SNP(1) = SNP(2) 'retain rurrent SNP CH(1) = CH(2) Loc(1) = Loc(2) Comp(1) = Comp(2) l = 1End SubPrivate Sub ShowStretch()A Cells(rowStart1 + k, colStart1 + 0) = SNP(1) 'the start point/ Cells(rowStart1 + k, colStart1 + 1) = CH(1)0 Cells(rowStart1 + k, colStart1 + 2) = Loc(1)+ Cells(rowStart1 + k, colStart1 + 3) = l k = k + 1? 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ORKȹ 95%CIL 95%CIU X2K|}ȹ X2_MH0o!"KȹKmaȹKӡȹKRZMȹKȹKȹKd)c-ӡȉ"KlȹKNVȹKkyMȹKCMȹK)c-@ȉ"K$ȹK(>ȹK;a.KRa.Kӡa.Ka.Kȹ T48@ K;ȹ0ӡ"Ku„ȹgetLOHsetSNPidsetCHsetLocsetLOHEqualCHEqualLOHKȹKkȹKa.KȹDK=ѣqcSҠDǬ`ngetSNPidgetCHgetLocK{iSK{ȹKȹKuȹXRZa.X zMa.K )Z If 1[ IK{a.Xl/a.J ^ IK i) K} EF,}`KRZM ,V`KKыKʭRW{ȉK{KыKʭыKыK@:R 8SNP tools: compare haplotypeKыK vKыK¢MыKzыW{KMKrKRZMыKQыKi)!fkȑ**i)?{1!f|})cKq)c-ȉ"K#T_)cK~)c-~ȉ"K)c-NVȉ"0#T_"Kӡ"!f{)c-maȉ"-u„ȉ"Kі vKіRKыKDыKfXыKыK}ыKыK v"g{ 8The longest common stretch: Kы >The longest common stretch is: KKMHыK{R!fz)c Wi)InteriorColorIndexKK`K-ȉ"K|}Ki)Kh-Iȉ"*i)KT !f )cK"KpKL" -ȉ"-Dȉ"Wi)KF)c-#T_ȉ"-ȉ"-ȉ"Kʭ1KKKk1KDK,KfEK9)c-ȉ"KKKCMKf)cKʦKK)cKȄK#T_K)c-fxȉ"KʭAKkyMAKAKʭAK'AK nKzAKCA DC:\Program Files\SNPHAP\Phase.EXE  LPHASE is not found in default folder.  8Please run PHASE by yourselfKCMAK1KAK}AW{* i) snp_1Name  TextFilePlatform8TextFileTrailingMinusNumbersBackgroundQueryK KLKӡAK>R1 .out.txt _freqs _pairsKAK1 6SNP tools: convert to PhaseK{KvKvK vKKLIK1K`vK`vK` v freq pairsKA Ko~ nKʭKAKޔ vKAK¢MAKQAKMKM nKRAK+KAKqAK  P  SW{KAKu„)c-ȉ"K`RKAKDAKfXAK  vK RKnAKmaAKAKv .PedPhase_work.out.transKȑ~K1Kʭȑ~ .out .out.transK1K'ȑ~Kzȑ~Kȑ~KĔ n "PedPhase_work.out PedPhase1KCȑ~K}ȑ~Kȑ~K{1 "PedPhase_work.txt PedPhase2KMȑ~ -b -c -l -m -iKO  6SNP data including pedigreeK  Kȑ~K@ȑ~K@  XSNP data including individual ID in 1st row!Kȑ~KNVȑ~ PedPhase.EXE  :Failure running PedPhase.exe.Kȑ~Kȑ~ WinPedPhase Kȑ~K n"g{1K{ȑ~KRȑ~KlKo~ȑ~Kdȑ~Kȑ~Kȑ~KL nK{KȹKRȹK?)cK{ȹ (Pedigree data of ID   not found!K ȹKȹKȹK ȹKxZMȹK)cKȹKdȹKȄȹK1ȹKCM)c-¢Mȉ"KȹK( ȹKȹKȹK4M)c _F _M |KRK  vK RKnȑ~Kmaȑ~KQȑ~KfXȑ~Kȑ~K@v $SNP tools: hotspotKȁlKPv vK{!mKPvvKPvvKȁlKȁlKȁlK¢MȁlW{!mKRZMȁlKQȁlKPvRKȁlKDȁlKfXȁlKȁlK}ȁlKȁlKٶv* i) SNP ID ChK.)c Location EϔΩ+ZVnJvgetCompsetComp EqualComp T48D ({bK)cW{bK{bK{b*})cK}"K)c0ʦ"K3)c-mȉ"- ȉ"K\)c-Mȉ"-ȉ"0V"K v-(ȉ"*d)cKȹj K{YkKȹjKmvKmvKm vKȹjK vKȹjKmaȹjK¢MȹjKHMvKHM vW{YkKRZMȹjKQȹjKۖ vKۖRKȹjKMvKMvKMRKM vKM vKMvKMvKDȹjKfXȹjKGȹjK}ȹjKȹjKwyv Chromosome DistanceKȹK(ȹKȹ({iSK{iSW{iS%s{Yk!fR)c*|})cK|}"CopyKȹK\ȹKȹK^ȹKQȹ!f)c KȹKMȹKo~ȹKȹKQiK1KQi v\Progra~1\Haploview\Haploview.jar -assocCC -check -pedfile   -info Kpٖ1 java -jar c: java -jar d: VHaploview is not found in default folders,  @Please run Haploview by yourselfK4Qi K1KNVQiKQiK1 .pedKQiK1KMQiKQiKʭQiKQiKM nKzQiK+QiKd nKCQiK}QiKd TSNP tools: convert Hapmart0.7 to HaploviewK{iK1KCMQiK'QiKp nKpKQiK¢MQiK}QiK1K1K1"g{iK{Qi KRQiK<KfXQiK1KIQiK1KmaQiKҋQiK1KxZMQiK1KYQiK¢M1KqQiW{i MARKER IDK.)c POSITION dCould not find column of 'marker id' or 'position'-ȉ" GENOTYPE FCould not find column of 'genotype' SampleKV)c-Tȉ"K*pKY vKYRKQiKDQiK vKRKnQiKmaQiKQQi  -info KQiK/-vK hK h 4 -assocCC -check -pedfile Kd1 FC:\Progra~1\Haploview\Haploview.exe  H FC:\Progra~2\Haploview\Haploview.exeK4 hKNV hK+S hK1K hKCM hK hKʭ hK' hKz hK+ hKٍ nKC hK} hKٍ LSNP tools: convert HAPMAP to HaploviewK{hK vK vK  vK{1KlvKlvKl vK} hK hK¢M h"g{hK{ h KR hK|FKfX hKؠ1K" hKma hKI hKҋ hKxZM hKxZM1KY hKq hW{h-ȉ"-Mȉ"K)cK vKRK hKD hK vKRKn hKma hKQ hK hKevKșcK 1KșcKP1K4șcKNVșcK+SșcKșcKCMșcKșcKʭșcK'șcKzșcK+șcKX nKCșcK}șcKX >SNP tools: convert to HaploviewK{YdK`UvIDK`UvK`U vK@1KMKP6vKP6vKP6 vK}șcKșcK¢Mșc"g{YdK{șc KRșcKLoKfXșcKD1KIșcKmașcKҋșcKxZMșcKqșcW{Yd*i) .INFO .mapKKK.ȉ"-ȉ"-ȉ"Ki)KӡșcK,)cKșcK,)c-Tȉ"K+)cKP vKPRKșcKDșcK vKRKnșcKmașcKQșcKșcK2v 2SNP tools: Common StretchKa]K vK{^KvKvKKa]K vKa]Ka]K¢Ma]K vK  vKQa]W{^KRZMa]Kla]Ki)*i)KWa]K|1K)c LengthK)c 0{^Ki)*i)Ka]KȄ)c0HM"K)cKgq)c0" K vKRKa]KDa]Strata_OR_Power99KStrata_OR_Power999KStrata_OR_Power9999KKfXa]Ka]K}a]Ka]Strata_OR_P_minor_HaploviewStrata_OR_P_HaploviewStrata_OR_PowerKHvDhFc\ F9m;Fz6#DF Worksheet#N،:|<9B)$b)MP4ƜEr^@AӡNinitF H48WpYStrata_OR_P_minorStrata_OR_Power95K d zMYW zMYW zM YW|}Y dYWnYWYW YW YWF-Y dF-YWF- Y d YW  YWY dYSIRWYW YW Y dY Strata_OR_PWYWY SIR_CI95L SIR_CI95U SIR_CI99L SIR_CI99U OddsRatioOR_minor OR_PowerKOR_PMHOR_Power OR_Power95 OR_Power99 OR_Power999 OR_Power9999 OR_Power99999Strata_OR_CI99U Strata_OR_X2Ka.Ka.KԪ ,`,A`%tA`K*p Strata_OR_CI95LStrata_OR_CI95UStrata_OR_CI99L%t` RiskRatioRR_CI95LRR_CI95URR_X2 RR_PowerK/BQNm) @/ACHV3+ Constructor <Kpa. 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Output for PedPhase$* Image1t{? 8 !@ PedPhase Call and LOH (sheet name must not contain space!)(2<Label2t1O$<RefEdit2 ,4CommandButton1d , 24progressBaro E( 2@Percent2 E(2<ProgressOE$* Image1ssO  Microsoft Forms 2.0 FormOBMECompObjyEVBFrame>frmLOHstretch|xJŽѿ7ÎѿfVERSION 5.00 Begin {C62A69F0-16DC-11CE-9E98-00AA00574A4F} frmOR Caption = "SNP tools: Odds Ratio (Mantel-Haenszel)" ClientHeight = 2235 ClientLeft = 30 ClientTop = 330 ClientWidth = 5550 StartUpPosition = 1 'CenterOwner TypeInfoVer = 28 End ,J  @}3&aR KQ8Arial Unicode MS8KEFҋB `EF (2<o{}CompObj~EVBFrameKfrmHotspotsÎѿÎѿ( Soruce dataq{5"Tahoma !H${5"Tahoma ( Result data{5"Tahoma H${5"Tahoma (Run{u"Tahoma"5"Tahoma6 w @"Tahoma*Progress5"Tahomass{{R KQlt ( @`c?`c?`c?`c?`p`wwwpwwwppffw~wvfpvgpp~f~v~o~o~owo~p~pw~ww~wwwwpp??Label1ssO <uRefEdit1 select data area inclluding 5 columns: SNPID, chromosome, location, Call and LOH (sheet name must not contain space!)(2<Label2t1O$<RefEdit2 ,4CommandButton1d , 24progressBaro E( 2@Percent2 E(2<ProgressOE$* Image1ssO  Microsoft Forms 2.0 FormOBMEVERSION 5.00 Begin {C62A69F0-16DC-11CE-9E98-00AA00574A4F} frmLOHstretch Caption = "SNP tools: find LOH>=2 stretch on chromosome" ClientHeight = 2232 ClientLeft = 36 ClientTop = 336 ClientWidth = 5544 StartUpPosition = 1 'CenterOwner TypeInfoVer = 28 End ,J  @}3&aR KQ8Arial Unicode MS8KEFҋB `EF (2<( Soruce dataq{5"Tahoma foCompObjEVBFrameG!H${5"Tahoma ( Result data{5"Tahoma H${5"Tahoma (Run{u"Tahoma"5"Tahoma6 w @"Tahoma*Progress5"Tahoma{{R KQlt ( @    6 !"#$%&'()*+,-./012345789:;<=>@BCDEGHcJKLMNOPQRSTUVWXYZ[\]^_`abdefghijklnpqrsuvxyz{|}~`c?`c?`c?`c?`p`wwwpwwwppffw~wvfpvgpp~f~v~o~o~owo~p~pw~ww~wwwwpp??Label1O <sRefEdit1 select data area inclluding 4 columns: SNPID, chromosome, location and feature (sheet name must not contain space!)(2<Label2t1O$<RefEdit2 ,4CommandButton1d , 24progressBaro E( 2@Percent2 E(2<ProgressOE$* Image1ssO  Microsoft Forms 2.0 FormOBMEVERSION 5.00 Begin {C62A69F0-16DC-11CE-9E98-00AA00574A4F} frmHotspots Caption = "SNP tools: find break points on chromosome" ClientHeight = 2232 ClientLeft = 36 ClientTop = 336 ClientWidth = 5544 StartUpPosition = 1 'CenterOwner TypeInfoVer = 28 End (  #}3&R KQ8Arial Unicode MS8KEFҋB `EF @(2<Lab( Soruce dataq{5"Tahoma !H${5"Tahoma (frmCompHapYÎѿCĎѿfoCompObj?E Result data{5"Tahoma H${5"Tahoma  ( Length Matrixo {u"Tahoma "5"Tahoma 6 w @"Tahoma *Progress5"Tahomass{{R KQlt ( @`c?`c?`c?`c?`p`wwwpwwwppffw~wvfpvgpp~f~v~o~o~owo~p~pw~ww~wwwwpp?? 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"#$%&(2<Label3ssO"P H&TextBox1 Assign a path and filename for output X 4&CommandButton2a !Assign a path and filename for output ($2<Label5x1O, %L OptionButton12a , &L OptionButton22a ,'T OptionButton15a ,(L OptionButton16a , )L OptionButton36a $*<RefEdit1  Microsoft Forms 2.0 FormOBMEVERSION 5.00 Begin {C62A69F0-16DC-11CE-9E98-00AA00574A4F} frmSTRshared Caption = "STR tools: Compare sharing STR allele" ClientHeight = 2244 ClientLeft = 60 ClientTop = 336 ClientWidth = 5544 StartUpPosition = 1 'CenterOwner TypeInfoVer = 80 End ,  /@U}% R KQ8Arial Unicode MS8KEFҋB `EFL(2<( SNP sourceoq5"Tahoma,Convert{w @"Tahomat"5"Tahomat6 w @"Tahomat*ProgfopCompObjEVBFrameNress5"Tahomass ( SNP info fileoq5"Tahomass @H,snp.info5"Tahomafo(...{4u"Tahoma ( SNP data fileq5"Tahoma @H,snp.ped5"Tahomad(...{4u"Tahoma , HAPLOVIEWVq{w @"Tahoma(SNP typeq5"Tahomape8F, 0ahoA, B, AB, Nocall5"Tahomape8F 0ahoACGT, Del, Hetd5"Tahomape ( SNP data fileoq5"Tahomape(SNP typeq5"Tahomape!H45"TahomapeLabel1peO$@Converte, 24progressBar ( 2<Percente  (2<ProgressO (2@Label3ssOhL @#TextBox1 >Don't use file name including space,4CommandButton2o!"(0@Label4x1O*L @ #TextBox2 Don't use file name including space,4 CommandButton3o!< !D  HAPLOVIEWttoRun Haploview3o((08 Label5x2O \ )1X 'OptionButton13o Genotype in the format of AA, AB and BBX *1X!OptionButton23o' Genotype in the format of A,T,C,Gand(+2@Label6x2Oq(.08Label7x2O /<hRefEdit1 aplease include columns of chromosome, position, marker id and genotype. 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frmHaploview Caption = "SNP tools: Convert SNP data to format of Haploview" ClientHeight = 4400 ClientLeVBFrameWfrmHapMapviewpɎѿ'ʎѿf)oft = 60 ClientTop = -8900.001 ClientWidth = 6000 StartUpPosition = 1 'CenterOwner TypeInfoVer = 91 End (  0Z}% R KQ8Arial Unicode MS(2<( SNP sourceoq5"Tahoma(Convert{u"Tahoma"5"Tahoma6     !"#$%&'()*+,-./012356789:;<=>?@ABCDEFGHIJKLMNOPQRSTUVWXY[\^_`abdefghijklmnopqrstuvwxyz{|}~w @"Tahoma*Progress5"Tahomass ( SNP info fileoq5"Tahomass @H,snp.info5"Tahomafo ( SNP data fileoq5"Tahomafo @H,snp.pedo5"Tahomado( HAPLOVIEWVq{u"Tahomado(SNP typeq5"Tahomape8F, 0ahoA, B, AB, Nocall5"Tahomape8F 0ahoACGT, Del, Hetd5"Tahomape ( SNP data fileoq5"Tahomape(SNP typeq5"Tahomape @H,{A1:K510e1Arial Unicode MSLabel10eO$8Converte, 24progressBard ( 2<Percente  (2<ProgressO (2@Label3ssOh$@TextBox1 >(0@Label4x1O*$@TextBox2 ( !< HAPLOVIEWard((08 Label5x2O 0 )1X OptionButton1 MS 0 *1X OptionButton2 MS' (+2@ Label6x2Oq(.08Label7x2O $0DRefEdit1 CompObjEVBFrameWPROJECTwm PROJECT4R 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Class=PedigreeItem Class=selectInfo Class=statusBarControler Class=SNPLOH Module=Standard_IR Module=OddsRatios Module=RiskRatios Class=MantelHaenszel Class=SNPsample Class=MHstrata Module=OddsRatioStrata BaseClass=frmPhase BaseClass=frmTransposeTextFile BaseClass=frmPedPhase BaseClass=frmOR BaseClass=frmLOHstretch BaseClass=frmHotspots BaseClass=frmCompHap BaseClass=frmCommonStretch Class=DieseArbeitsmappe Class=Affy_anno_gene BaseClass=frmSTRshared Module=R BaseClass=frmHapMart07 BaseClass=frmHaploview BaseClass=frmHapMapview Module=OddsRatioHaploview Name="VBAProject" HelpContextID="0" CMG="5B595DF30DF70DF70DF70DF7" DPB="070501A701FFAC00AC00AC" GC="B3B1B51B601C601C9F" [Host Extender Info] &H00000001={3832D640-CF90-11CF-8E43-00A0C911005A};VBE;&H00000000 [Workspace] ThisWorkbook=254, 0, 834, 397, C Sheet1=0, 0, 0, 0, C SNP_function=259, 183, 1024, 608, C SNPData=0, 0, 0, 0, C Base=280, 26, 860, 423, C ABC=0, 0, 0, 0, C frmSNPHAP=280, 26, 860, 423, C, 100, 100, 1059, 752, C rangeInfo=0, 0, 0, 0, C PedigreeItem=0, 0, 0, 0, C selectInfo=0, 0, 0, 0, C statusBarControler=410, 156, 990, 553, C SNPLOH=0, 0, 0, 0, C Standard_IR=0, 0, 0, 0, C OddsRatios=0, 0, 0, 0, C RiskRatios=0, 0, 0, 0, C MantelHaenszel=0, 0, 0, 0, C SNPsample=0, 0, 0, 0, C MHstrata=0, 0, 0, 0, C OddsRatioStrata=0, 0, 0, 0, C frmPhase=332, 78, 912, 475, C, 300, 300, 1259, 952, C frmTransposeTextFile=306, 52, 886, 449, C, 281, 120, 1155, 606, C frmPedPhase=358, 104, 938, 501, C, 200, 200, 1159, 852, C frmOR=0, 0, 0, 0, C, 233, 172, 1082, 633, C frmLOHstretch=0, 0, 0, 0, C, 25, 25, 984, 677, C frmHotspots=0, 0, 0, 0, C, 125, 125, 1084, 777, C frmCompHap=0, 0, 0, 0, C, 50, 50, 1009, 702, C frmCommonStretch=0, 0, 0, 0, C, 0, 0, 959, 652, C DieseArbeitsmappe=0, 0, 0, 0, C Affy_anno_gene=0, 0, 0, 0, C frmSTRshared=0, 0, 0, 0, C, 250, 250, 1209, 902, C R=0, 0, 0, 0, C frmHapMart07=384, 127, 964, 524, C, 275, 329, 1024, 660, C frmHaploview=252, 0, 1273, 842, , 434, 225, 749, 484, frmHapMapview=332, 105, 912, 501, 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