NAME

       getGeneExpression - compute expression of whole genes

SYNOPSIS

       getGeneExpression -o <outFileName> -t <trInfoFileName>  [OPTIONS] [samplesFile]

DESCRIPTION

       Computes expression of whole genes.

              [samplesFile] should contain transposed MCMC samples which will be transformed into
              gene expression samples.

OPTIONS

       --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)