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)