estimateDE - this bitseq module estimates differential expression
from data sets
estimateDE -o <outFilePrefix> -p
<parFileName> [OPTIONS] [sampleFiles]
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
--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)