estimateDE

this bitseq module estimates differential expression from data sets

Provided by: bitseq (Version: 0.7.5+dfsg-6)
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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)