bionic (1) estimateVBExpression.1.gz

NAME

       estimateVBExpression - estimate expression given precomputed probabilities of (observed) reads alignments

SYNOPSIS

       estimateVBExpression -o <outFilePrefix>  [OPTIONS] [prob file]

DESCRIPTION

       Estimates expression given precomputed probabilities of (observed) reads' alignments.

              Uses Variational Bayes algorithm to produce parameters for distribution of relative abundances.

OPTIONS

       --help

              Show this help information.

       --optLimit=<limit>

              Optimisation limit in terms of minimal gradient or change of bound. (default: 1e-05)

       --maxIter=<maxIter>

              Maximum number of iterations. (default: 10000)

       -m <optMethod> ,   --method=<optMethod>

              Optimization method (steepest, PR, FR, HS). (default: FR)

       -o <outFilePrefix> ,   --outPrefix=<outFilePrefix>

              Prefix for the output files.

       -O <outputType> ,   --outType=<outputType>

              Output type (theta, RPKM, counts) of the samples sampled from the distribution. (default: theta)

       -P <procN> ,   --procN=<procN>

              Limit the maximum number of threads to be used. (default: 4)

       --samples=<samples>

              Number of samples to be sampled from the distribution.

       -s <seed> ,   --seed=<seed>

              Random initialization seed.

       -t <trInfoFileName> ,   --trInfoFile=<trInfoFileName>

              File containing transcript information. (Necessary for RPKM samples)

       -v ,   --verbose

              Verbose output. (default: Off)

       -V ,   --veryVerbose

              More verbose output, better if output forwarded into file. (default: Off)