getGeneExpression - compute expression of whole genes
getGeneExpression -o <outFileName> -t
<trInfoFileName> [OPTIONS] [samplesFile]
Computes expression of whole genes.
- [samplesFile] should contain transposed MCMC samples which will be
transformed into gene expression samples.
--help
- Show this help information.
-a , --adjustByLength
- Adjust expression by transcripts length. (default: Off)
-g <geneInfoFile> ,
--geneInfoFile=<geneInfoFile>
- Name of while to which gene information will be saved.
-G <geneListFile> ,
--geneList=<geneListFile>
- Name of the file containing list of gene names (one for each
transcript).
-l , --log
- Output logged values. (default: Off)
-o <outFileName> ,
--outFile=<outFileName>
- Name of the output file.
--theta2rpkm
- Transform transcript expression in theta to gene expression in RPKM.
(default: Off)
-t <trInfoFileName> ,
--trInfoFile=<trInfoFileName>
- Name of the transcript file.
-T <trMapFile> ,
--trMap=<trMapFile>
- Name of the file containing transcript to gene mapping.
--updateTrFile
- Update trInfoFile if new gene names were provided (with trMapFile or
geneListFile). (default: Off)
-v , --verbose
- Verbose output. (default: Off)