.\" DO NOT MODIFY THIS FILE!  It was generated by help2man 1.47.11.
.TH ESTIMATEVBEXPRESSION "1" "September 2019" "estimateVBExpression 0.7.5+dfsg" "User Commands"
.SH NAME
estimateVBExpression \- estimate expression given precomputed probabilities of (observed) reads alignments
.SH SYNOPSIS
.B estimateVBExpression
\fI\,-o <outFilePrefix>  \/\fR[\fI\,OPTIONS\/\fR] [\fI\,prob file\/\fR]
.SH DESCRIPTION
Estimates expression given precomputed probabilities of (observed) reads' alignments.
.IP
Uses Variational Bayes algorithm to produce parameters for distribution of relative abundances.
.SH OPTIONS
.HP
\fB\-\-help\fR
.IP
Show this help information.
.HP
\fB\-\-optLimit=\fR<limit>
.IP
Optimisation limit in terms of minimal gradient or change of bound. (default: 1e\-05)
.HP
\fB\-\-maxIter=\fR<maxIter>
.IP
Maximum number of iterations. (default: 10000)
.HP
\fB\-m\fR <optMethod> ,   \fB\-\-method=\fR<optMethod>
.IP
Optimization method (steepest, PR, FR, HS). (default: FR)
.HP
\fB\-o\fR <outFilePrefix> ,   \fB\-\-outPrefix=\fR<outFilePrefix>
.IP
Prefix for the output files.
.HP
\fB\-O\fR <outputType> ,   \fB\-\-outType=\fR<outputType>
.IP
Output type (theta, RPKM, counts) of the samples sampled from the distribution. (default: theta)
.HP
\fB\-P\fR <procN> ,   \fB\-\-procN=\fR<procN>
.IP
Limit the maximum number of threads to be used. (default: 4)
.HP
\fB\-\-samples=\fR<samples>
.IP
Number of samples to be sampled from the distribution.
.HP
\fB\-s\fR <seed> ,   \fB\-\-seed=\fR<seed>
.IP
Random initialization seed.
.HP
\fB\-t\fR <trInfoFileName> ,   \fB\-\-trInfoFile=\fR<trInfoFileName>
.IP
File containing transcript information. (Necessary for RPKM samples)
.HP
\fB\-v\fR ,   \fB\-\-verbose\fR
.IP
Verbose output. (default: Off)
.HP
\fB\-V\fR ,   \fB\-\-veryVerbose\fR
.IP
More verbose output, better if output forwarded into file. (default: Off)