NAME

       estimateDE - this bitseq module estimates differential expression from data sets

SYNOPSIS

       estimateDE -o <outFilePrefix> -p <parFileName>  [OPTIONS] [sampleFiles]

DESCRIPTION

       Estimate differential expression from the dataset.

              [sampleFiles]  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.

       --confidenceInterval=<cf>

              Percentage for confidence intervals. (default: 95)

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

              Parameter lambda_0. (default: 2)

       --norm=<normalization>

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

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

              Prefix for the output files.

       -p <parFileName> ,   --parameters=<parFileName>

              File containing estimated hyperparameters.

       -s ,   --samples

              Produce samples of condition mean expression apart from PPLR and confidence. (default: Off)

       --seed=<seed>

              Random initialization seed.

       -v ,   --verbose

              Verbose output. (default: Off)