NAME
estimateHyperPar - estimate expression dependent hyperparameters for bitseq
SYNOPSIS
estimateHyperPar -o <outFileName> [OPTIONS] [sampleFiles]
DESCRIPTION
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
OPTIONS
--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)