.\" DO NOT MODIFY THIS FILE!  It was generated by help2man 1.47.11.
.TH ESTIMATEHYPERPAR "1" "September 2019" "estimateHyperPar 0.7.5+dfsg" "User Commands"
.SH NAME
estimateHyperPar \- estimate expression dependent hyperparameters for bitseq
.SH SYNOPSIS
.B estimateHyperPar
\fI\,-o <outFileName>  \/\fR[\fI\,OPTIONS\/\fR] [\fI\,sampleFiles\/\fR]
.SH DESCRIPTION
Estimate expression dependent hyperparameters from the dataset.
.IP
[sample Files] should contain transposed MCMC samples from replicates.
To distinguish conditions use C between them e.g.:
.IP
samplesC1\-R1.rpkm samplesC1\-R2.rpkm C samplesC2\-R1.rpkm samplesC2\-R2.rpkm
.SH OPTIONS
.HP
\fB\-\-help\fR
.IP
Show this help information.
.HP
\fB\-\-exThreshold=\fR<exT>
.IP
Threshold of lowest expression for which the estimation is done. (default: \fB\-5\fR)
.HP
\fB\-g\fR <groupsN> ,   \fB\-\-groupsNumber=\fR<groupsN>
.IP
Number of groups of transcript of similar size. (default: 200)
.HP
\fB\-l\fR <lambda0> ,   \fB\-\-lambda0=\fR<lambda0>
.IP
Precision scaling parameter lambda0. (default: 2)
.HP
\fB\-\-lowess\-f=\fR<lowess\-f>
.IP
Parameter F for lowess smoothing specifying amount of smoothing. (default: 0.2)
.HP
\fB\-\-lowess\-steps=\fR<lowess\-steps>
.IP
Parameter Nsteps for lowess smoothing specifying number of iterations. (default: 5)
.HP
\fB\-\-meanFile=\fR<meanFileName>
.IP
Name of the file containing joint mean and variance.
.HP
\fB\-\-noforce\fR
.IP
Do not force smoothing of the parameters. (default: Off)
.HP
\fB\-\-norm=\fR<normalization>
.IP
Normalization constants for each input file provided as comma separated list of doubles (e.g. 1.0017,1.0,0.9999 ).
.HP
\fB\-o\fR <outFileName> ,   \fB\-\-outFile=\fR<outFileName>
.IP
Name of the output file.
.HP
\fB\-p\fR <paramsAllFileName> ,   \fB\-\-paramsAllFile=\fR<paramsAllFileName>
.IP
Name of the file to which to store all parameter values generated prior to lowess smoothing.
.HP
\fB\-s\fR <samplesN> ,   \fB\-\-samplesNumber=\fR<samplesN>
.IP
Number of samples generated for each group. (default: 2)
.HP
\fB\-\-seed=\fR<seed>
.IP
Random initialization seed.
.HP
\fB\-S\fR ,   \fB\-\-smoothOnly\fR
.IP
Input file contains previously sampled hyperparameters which should smoothed only. (default: Off)
.HP
\fB\-v\fR ,   \fB\-\-verbose\fR
.IP
Verbose output. (default: Off)
.HP
\fB\-V\fR ,   \fB\-\-veryVerbose\fR
.IP
More verbose output. (default: Off)