#BFRMFactor
#Wed Jan 05 18:29:43 GMT-06:00 2011
JVMLevel=
LSID=urn\:lsid\:8080.genepattern.megatron.uth.tmc.edu\:genepatternmodules\:929\:6
author=Jeffrey Chang, Carlos Carvalho, Joseph Nevins, Mike West, Duke University
commandLine=/usr/local/bin/python /opt/SIGNATURE/bfrmfactor.py --python\=/usr/local/bin/python --bfrm_bin\=/opt/SIGNATURE/bfrm64 --arrayplot\=/opt/SIGNATURE/arrayplot.py --cluster\=/usr/local/bin/cluster --libpath\=/opt/SIGNATURE -z <filter_mean> <filter_var> <num_control_vars> <nucleus_file> <start_factors> <max_factors> <max_genes> <dataset>\r\n
cpuType=any
description=BFRM Factor Model
fileFormat=
language=any
name=BFRMFactor
os=any
p1_MODE=IN
p1_TYPE=FILE
p1_default_value=
p1_description=Gene expression data (GCT, PCL, and some other formats) that you wish to factor.
p1_fileFormat=gct;pcl
p1_name=dataset
p1_optional=
p1_prefix_when_specified=
p1_type=java.io.File
p1_value=
p2_default_value=
p2_description=Before factoring, filter out this portion of genes with the lowest mean expression value (0.0-1.0).
p2_fileFormat=
p2_name=filter_mean
p2_optional=on
p2_prefix_when_specified=--filter_mean\=
p2_type=java.lang.Float
p2_value=
p3_default_value=
p3_description=Before factoring, filter out this portion of genes with the lowest variance (0.0-1.0).
p3_fileFormat=
p3_name=filter_var
p3_optional=on
p3_prefix_when_specified=--filter_var\=
p3_type=java.lang.Float
p3_value=
p4_default_value=
p4_description=Use this many control variables.  The AFFX control probes must be in your data set.
p4_fileFormat=
p4_name=num_control_vars
p4_optional=on
p4_prefix_when_specified=--nc\=
p4_type=java.lang.Integer
p4_value=
p5_MODE=IN
p5_TYPE=FILE
p5_default_value=
p5_description=Do an evolutionary analysis that is nucleated from these genes.  This text file should contain gene IDs that I will match to those in the data set.
p5_fileFormat=
p5_name=nucleus_file
p5_optional=on
p5_prefix_when_specified=--nucleus_file\=
p5_type=java.io.File
p5_value=
p6_default_value=
p6_description=Initiate the analysis with this number of latent factors.
p6_fileFormat=
p6_name=start_factors
p6_optional=on
p6_prefix_when_specified=--num_factors\=
p6_type=java.lang.Integer
p6_value=
p7_default_value=
p7_description=In an evolutionary analysis, stop when this number of factors is reached.
p7_fileFormat=
p7_name=max_factors
p7_optional=on
p7_prefix_when_specified=--evol_max_factors\=
p7_type=java.lang.Integer
p7_value=
p8_default_value=
p8_description=In an evolutionary analysis, stop when this number of genes is reached.
p8_fileFormat=
p8_name=max_genes
p8_optional=on
p8_prefix_when_specified=--evol_max_genes\=
p8_type=java.lang.Integer
p8_value=
pipelineModel=
privacy=public
quality=development
requiredPatchLSIDs=
requiredPatchURLs=
serializedModel=
taskType=SIGNATURE
userid=
version=
