estimateHyperPar - estimate expression dependent hyperparameters
for bitseq
estimateHyperPar -o <outFileName>
[OPTIONS] [sampleFiles]
Estimate expression dependent hyperparameters from the
dataset.
- [sample Files] 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.
--exThreshold=<exT>
- Threshold of lowest expression for which the estimation is done. (default:
-5)
-g <groupsN> ,
--groupsNumber=<groupsN>
- Number of groups of transcript of similar size. (default: 200)
-l <lambda0> ,
--lambda0=<lambda0>
- Precision scaling parameter lambda0. (default: 2)
--lowess-f=<lowess-f>
- Parameter F for lowess smoothing specifying amount of smoothing. (default:
0.2)
--lowess-steps=<lowess-steps>
- Parameter Nsteps for lowess smoothing specifying number of iterations.
(default: 5)
--meanFile=<meanFileName>
- Name of the file containing joint mean and variance.
--noforce
- Do not force smoothing of the parameters. (default: Off)
--norm=<normalization>
- Normalization constants for each input file provided as comma separated
list of doubles (e.g. 1.0017,1.0,0.9999 ).
-o <outFileName> ,
--outFile=<outFileName>
- Name of the output file.
-p <paramsAllFileName> ,
--paramsAllFile=<paramsAllFileName>
- Name of the file to which to store all parameter values generated prior to
lowess smoothing.
-s <samplesN> ,
--samplesNumber=<samplesN>
- Number of samples generated for each group. (default: 2)
--seed=<seed>
- Random initialization seed.
-S , --smoothOnly
- Input file contains previously sampled hyperparameters which should
smoothed only. (default: Off)
-v , --verbose
- Verbose output. (default: Off)
-V , --veryVerbose
- More verbose output. (default: Off)