GETWITHINGENEEXPRESSION

NAME

getWithinGeneExpression - compute relative expression of transcripts within genes

SYNOPSIS

getWithinGeneExpression -t <trInfoFileName> [OPTIONS] [samplesFile]

DESCRIPTION

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].

OPTIONS

--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)