.\" DO NOT MODIFY THIS FILE!  It was generated by help2man 1.47.11.
.TH GETWITHINGENEEXPRESSION "1" "September 2019" "getWithinGeneExpression 0.7.5+dfsg" "User Commands"
.SH NAME
getWithinGeneExpression \- compute relative expression of transcripts within genes
.SH SYNOPSIS
.B getWithinGeneExpression
\fI\,-t <trInfoFileName>  \/\fR[\fI\,OPTIONS\/\fR] [\fI\,samplesFile\/\fR]
.SH DESCRIPTION
Computes relative expression of transcripts within genes.
.IP
[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].
.SH OPTIONS
.HP
\fB\-\-help\fR
.IP
Show this help information.
.HP
\fB\-a\fR ,   \fB\-\-adjustByLength\fR
.IP
Adjust expression by transcripts length. (default: Off)
.HP
\fB\-G\fR <geneListFile> ,   \fB\-\-geneList=\fR<geneListFile>
.IP
Name of the file containing list of gene names (one for each transcript).
.HP
\fB\-\-groupByGene\fR
.IP
Group transcripts by genes (this can change the default order of output. (default: Off)
.HP
\fB\-l\fR ,   \fB\-\-log\fR
.IP
Use logged values. (default: Off)
.HP
\fB\-o\fR <outFileName> ,   \fB\-\-outFile=\fR<outFileName>
.IP
Name of the output file.
.HP
\fB\-s\fR <sumFileName> ,   \fB\-\-sumFile=\fR<sumFileName>
.IP
Name of summarization file where true mean, true variance and relative mean and relative variance are saved.
.HP
\fB\-t\fR <trInfoFileName> ,   \fB\-\-trInfoFile=\fR<trInfoFileName>
.IP
Name of the transcript file.
.HP
\fB\-T\fR <trMapFile> ,   \fB\-\-trMap=\fR<trMapFile>
.IP
Name of the file containing transcript to gene mapping.
.HP
\fB\-\-updateTrFile\fR
.IP
Update trInfoFile if new gene names were provided (with trMapFile or geneListFile). (default: Off)
.HP
\fB\-v\fR ,   \fB\-\-verbose\fR
.IP
Verbose output. (default: Off)