5.3 QTLClustInfo

When a QTL clustering has been done using QTLClust See QTLCLust, the result can be formatted using QTLClustInfo. This program allows user to get for a given trait, a given chromosome and a given clustering model, tables in which the results are summarized. QTLClustInfo computes also extra statistics as mahalanobis distances between the QTL of the clustering model, the unconditional confidence intervals (UCI) of these QTL and the predicted values of the observed QTL according to the clustering model.

5.3.1 Command Line Options

Option	Usage	Type	Explanation
-o,--output	required	string	The output file
-c,--chr	required	string	The name of the chromosome.
-t,--trait	required	string	The name of the trait.
-r,--clust	required	string	The clustering result file.
-b,--best	required	integer	The number of QTL for the best model.
--kmin	required	integer	The minimal value to compute the UCI.
--kmax	required	integer	The maximal value to compute the UCI.

For example, we focus on the chromosome `8' for the trait called `FT' for which we have previously performed a QTL clustering via QTLClust. We want to display the result of the clustering for the best model supposed to be the model with 5 QTL. We also want to compute the UCI by averaging over the clustering models from 1 QTL to 10 QTL. Thus we use the command

%java org.metatqtl.main.QTLClustInfo \ > -c 8 -t FT -r clust_res.txt -b 5 --kmin 1 --kmax 10 -o table.txt

The result of this command is dumped into the file table.txt which looks like this

## # Meta-QTL Table ## -- QTL Position Weight Distance CI(95%) UCI(95%) -- 1 14.64 0.06 6.21 11.72 11.72 2 75.39 0.37 1.26 6.25 8.97 3 89.68 0.42 2.64 3.79 4.24 4 114.47 0.07 5.2 11.14 11.62 5 165.25 0.09 - 13.86 13.86 -- ## # Observed QTL Table ## -- QTL Position CI(95%) Predicted Memberships 1 --> 5 -- Pioneer_HT_1 1.91 20.46 14.64 1 0 0 0 0 Poupard_2001_DPS_10 20.85 14.31 14.64 1 0 0 0 0 Pioneer_HT_2 62.7 24.62 75.39 0 1 0 0 0 Lubberstedt_1997_HT_17 74.15 14.31 75.39 0 1 0 0 0 Bouchez_2002_SD_1 74.86 14.31 75.39 0 1 0 0 0 Poupard_2001_DPS_11 76.1 16.7 75.53 0 0.99 0.01 0 0 Moreau_1998_SD_5 67.72 28.62 75.68 0 0.98 0.02 0 0 Bohn_2000_DPS_11 79.23 14.9 75.96 0 0.96 0.04 0 0 Vladutu_1999_DPS_2 73.04 26.26 76.1 0 0.95 0.05 0 0 Rebai_1997_SD_18 59.86 63.15 78.96 0 0.75 0.25 0 0 Chardon_2005b_SD_1 70.96 73.74 81.64 0 0.58 0.41 0.01 0 Charcosset_unpub_SD_7 71.13 71.42 81.64 0 0.58 0.41 0.01 0 Chardon_2005b_DPS_1 70.96 74.75 81.78 0 0.57 0.42 0.01 0 Groh_1998_HT_6 81.08 32.61 81.96 0 0.54 0.46 0 0 Mechin_2001_SD_4 82.66 21.44 83.25 0 0.45 0.55 0 0 Rebai_1997_SD_4 83.22 27.4 83.68 0 0.42 0.58 0 0 Rebai_1997_SD_31 83.96 30.97 84.11 0 0.39 0.61 0 0 Blanc_SXflofch8 85.04 37.98 84.39 0 0.37 0.63 0 0 Chardon_2005b_DPS_2 90.64 75.22 84.49 0 0.37 0.58 0.04 0 Chardon_2005b_SD_2 90.64 47.75 86.17 0 0.28 0.7 0.02 0 Groh_1998_SD_5 87.6 29.56 86.82 0 0.2 0.8 0 0 Blanc_SDflofch8 91.05 25.99 88.97 0 0.05 0.95 0 0 Moreau_1998_SD_6 93.8 11.92 89.68 0 0 1 0 0 Vladutu_1999_DPS_1 88.39 10.15 89.68 0 0 1 0 0 Chardon_2005a_SD_1 91.39 14.31 89.68 0 0 1 0 0 Chardon_2005a_DPS_1 91.39 7.13 89.68 0 0 1 0 0 Barierre_2005_SD_3 87.52 9.53 89.68 0 0 1 0 0 Vladutu_1999_HT_1 88.39 10.15 89.68 0 0 1 0 0 Blanc_SFflofch8 103.31 31.01 95.64 0 0.01 0.79 0.21 0 Pioneer_HT_3 112.74 12.31 114.47 0 0 0 1 0 Ribaut_1996_SD_4 126.15 28.46 114.47 0 0 0 1 0 Pioneer_HT_4 169.52 19.01 165.25 0 0 0 0 1 Cardinal_2001_DPS_7 167.11 45.98 165.25 0 0 0 0 1 Lubberstedt_1997_HT_16 156.52 26.22 165.25 0 0 0 0 1 --