getPPLR - compute PPLR from MCMC expression samples
getPPLR -o <outFileName> [OPTIONS]
[sampleFile-C1] [sampleFile-C1]
Computes PPLR from MCMC expression samples.
- (the probability of second condition being up-regulated) Also computes
log2 fold change with confidence intervals, and condition mean log
expression. [sampleFiles] should contain transposed MCMC samples from
different conditions.
--help
- Show this help information.
-d , --distribution
- Produce whole distribution of differences. (default: Off)
--inputIsLogged
- Indicate that the input expression estimates are on log scale. (Not
necessary to use with data generated by BitSeq-0.5.0 and above.) (default:
Off)
-o <outFileName> ,
--outFile=<outFileName>
- Name of the output file.
-s <selectFileName> ,
--selectFile=<selectFileName>
- File containing list of selected transcript IDs (zero based), only these
will be reported. Only works with --distribution option.
--subSample=<subSample>
- Sub-sample the distributions using a given fraction of expression samples.
(default: 1)
-v , --verbose
- Verbose output. (default: Off)