Man page - estimatehyperpar(1)

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Package: bitseq
apt-get install bitseq

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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)