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| #NearestTemplatePrediction | ||
| #Tue Jan 13 15:01:33 EST 2009 | ||
| JVMLevel= | ||
| author=Yujin Hoshida (Broad Institute) | ||
| commandLine=<R3.1_Rscript> <libdir>NTPez.R <input.exp.filename> <input.features.filename> <output.name> <distance.selection> <weight.genes> <num.resamplings> <GenePattern.output> <random.seed> | ||
| cpuType=any | ||
| description=Nearest neighbor prediction based on a list of marker genes | ||
| fileFormat=gct;png;txt;xls;cls | ||
| language=R-3.1.3 | ||
| name=NearestTemplatePrediction | ||
| os=any | ||
|
|
||
| p1_MODE=IN | ||
| p1_TYPE=FILE | ||
| p1_default_value= | ||
| p1_description=Gene expression data set (.gct) | ||
| p1_fileFormat=gct | ||
| p1_name=input.exp.filename | ||
| p1_optional= | ||
| p1_prefix_when_specified= | ||
| p1_type=java.io.File | ||
| p1_value= | ||
|
|
||
| p2_MODE=IN | ||
| p2_TYPE=FILE | ||
| p2_default_value= | ||
| p2_description=List of marker genes (.txt)\: Probe ID, Gene name, Class (1,2,...), Weight (optional) | ||
| p2_fileFormat=txt | ||
| p2_name=input.features.filename | ||
| p2_optional= | ||
| p2_prefix_when_specified= | ||
| p2_type=java.io.File | ||
| p2_value= | ||
|
|
||
| p3_default_value=NTP | ||
| p3_description=Name for output files | ||
| p3_fileFormat= | ||
| p3_name=output.name | ||
| p3_optional= | ||
| p3_prefix_when_specified= | ||
| p3_type=java.lang.String | ||
| p3_value= | ||
|
|
||
| p4_default_value=cosine | ||
| p4_description=Distance metric | ||
| p4_fileFormat= | ||
| p4_name=distance.selection | ||
| p4_optional= | ||
| p4_prefix_when_specified= | ||
| p4_type=java.lang.String | ||
| p4_value=cosine\=cosine;correlation\=correlation | ||
|
|
||
| p5_default_value=T | ||
| p5_description=Weight genes? (by statistic, fold change, etc. only for 2 classes) | ||
| p5_fileFormat= | ||
| p5_name=weight.genes | ||
| p5_optional= | ||
| p5_prefix_when_specified= | ||
| p5_type=java.lang.String | ||
| p5_value=T\=yes;F\=no | ||
|
|
||
| p6_default_value=1000 | ||
| p6_description=\# resampling to generate null distribution for distance metric | ||
| p6_fileFormat= | ||
| p6_name=num.resamplings | ||
| p6_optional= | ||
| p6_prefix_when_specified= | ||
| p6_type=java.lang.Integer | ||
| p6_value= | ||
|
|
||
| p7_default_value=F | ||
| p7_description=Create .gct and .cls files for GenePattern | ||
| p7_fileFormat= | ||
| p7_name=GenePattern.output | ||
| p7_optional= | ||
| p7_prefix_when_specified= | ||
| p7_type=java.lang.String | ||
| p7_value=T\=yes;F\=no | ||
|
|
||
| p8_default_value=7392854 | ||
| p8_description=Random seed | ||
| p8_fileFormat= | ||
| p8_name=random.seed | ||
| p8_optional= | ||
| p8_prefix_when_specified= | ||
| p8_type=java.lang.Integer | ||
| p8_value= | ||
|
|
||
| pipelineModel= | ||
| privacy=public | ||
| quality=preproduction | ||
| taskDoc=doc.html | ||
| requiredPatchLSIDs= | ||
| requiredPatchURLs= | ||
| serializedModel= | ||
| taskType=Prediction | ||
| userid=hoshida@broad.mit.edu | ||
| version=Updated to use R-3.1 and added HTML documentation. |