NAME

       estimateHyperPar - estimate expression dependent hyperparameters for bitseq

SYNOPSIS

       estimateHyperPar -o <outFileName>  [OPTIONS] [sampleFiles]

DESCRIPTION

       Estimate expression dependent hyperparameters from the dataset.

              [sample  Files]  should  contain  transposed  MCMC  samples  from  replicates.   To
              distinguish conditions use C between them e.g.:

              samplesC1-R1.rpkm samplesC1-R2.rpkm C samplesC2-R1.rpkm samplesC2-R2.rpkm

OPTIONS

       --help

              Show this help information.

       --exThreshold=<exT>

              Threshold of lowest expression for which the estimation is done. (default: -5)

       -g <groupsN> ,   --groupsNumber=<groupsN>

              Number of groups of transcript of similar size. (default: 200)

       -l <lambda0> ,   --lambda0=<lambda0>

              Precision scaling parameter lambda0. (default: 2)

       --lowess-f=<lowess-f>

              Parameter F for lowess smoothing specifying amount of smoothing. (default: 0.2)

       --lowess-steps=<lowess-steps>

              Parameter Nsteps for lowess smoothing specifying number of iterations. (default: 5)

       --meanFile=<meanFileName>

              Name of the file containing joint mean and variance.

       --noforce

              Do not force smoothing of the parameters. (default: Off)

       --norm=<normalization>

              Normalization constants for each input file provided as  comma  separated  list  of
              doubles (e.g. 1.0017,1.0,0.9999 ).

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

              Name of the output file.

       -p <paramsAllFileName> ,   --paramsAllFile=<paramsAllFileName>

              Name  of  the file to which to store all parameter values generated prior to lowess
              smoothing.

       -s <samplesN> ,   --samplesNumber=<samplesN>

              Number of samples generated for each group. (default: 2)

       --seed=<seed>

              Random initialization seed.

       -S ,   --smoothOnly

              Input file contains previously sampled hyperparameters which should smoothed  only.
              (default: Off)

       -v ,   --verbose

              Verbose output. (default: Off)

       -V ,   --veryVerbose

              More verbose output. (default: Off)