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)