getWithinGeneExpression - compute relative expression of
transcripts within genes
getWithinGeneExpression -t <trInfoFileName>
[OPTIONS] [samplesFile]
Computes relative expression of transcripts within genes.
- [samplesFile] should contain transposed MCMC expression samples. program
can produce means and variance and write them into [sumFile] or individual
MCMC samples which are written into [outFile].
--help
- Show this help information.
-a , --adjustByLength
- Adjust expression by transcripts length. (default: Off)
-G <geneListFile> ,
--geneList=<geneListFile>
- Name of the file containing list of gene names (one for each
transcript).
--groupByGene
- Group transcripts by genes (this can change the default order of output.
(default: Off)
-l , --log
- Use logged values. (default: Off)
-o <outFileName> ,
--outFile=<outFileName>
- Name of the output file.
-s <sumFileName> ,
--sumFile=<sumFileName>
- Name of summarization file where true mean, true variance and relative
mean and relative variance are saved.
-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)