NAME

       getPPLR - compute PPLR from MCMC expression samples

SYNOPSIS

       getPPLR -o <outFileName>  [OPTIONS] [sampleFile-C1] [sampleFile-C1]

DESCRIPTION

       Computes PPLR from MCMC expression samples.

              (the  probability  of  second condition being up-regulated) Also computes log2 fold
              change with confidence intervals, and condition mean log expression.  [sampleFiles]
              should contain transposed MCMC samples from different conditions.

OPTIONS

       --help

              Show this help information.

       -d ,   --distribution

              Produce whole distribution of differences. (default: Off)

       --inputIsLogged

              Indicate  that  the  input expression estimates are on log scale. (Not necessary to
              use with data generated by BitSeq-0.5.0 and above.) (default: Off)

       -o <outFileName> ,   --outFile=<outFileName>

              Name of the output file.

       -s <selectFileName> ,   --selectFile=<selectFileName>

              File containing list of selected transcript IDs (zero based), only  these  will  be
              reported. Only works with --distribution option.

       --subSample=<subSample>

              Sub-sample  the  distributions  using  a  given  fraction  of  expression  samples.
              (default: 1)

       -v ,   --verbose

              Verbose output. (default: Off)