.\" DO NOT MODIFY THIS FILE!  It was generated by help2man 1.47.11.
.TH ESTIMATEEXPRESSION "1" "September 2019" "estimateExpression 0.7.5+dfsg" "User Commands"
.SH NAME
estimateExpression \- estimate expression given precomputed probabilities of (observed) reads alignments
.SH SYNOPSIS
.B estimateExpression
\fI\,-o <outFilePrefix>  \/\fR[\fI\,OPTIONS\/\fR] [\fI\,prob file\/\fR]
.SH DESCRIPTION
Estimates expression given precomputed probabilities of (observed) reads' alignments.
.IP
Uses MCMC sampling algorithm to produce relative abundance or RPKM.
.SH OPTIONS
.HP
\fB\-\-help\fR
.IP
Show this help information.
.HP
\fB\-\-MCMC_burnIn=\fR<MCMC_burnIn>
.IP
Length of sampler's burn in period. (default: 1000)
.HP
\fB\-\-MCMC_chainsN=\fR<MCMC_chainsN>
.IP
Number of parallel chains used. At least two chains will be used. (default: 4)
.HP
\fB\-\-MCMC_dirAlpha=\fR<MCMC_dirAlpha>
.IP
Alpha parameter for the Dirichlet distribution. (default: 1)
.HP
\fB\-\-MCMC_samplesDOmax\fR
.IP
Produce maximum number of samples (samplesNmax) in second iteration and quit. (default: Off)
.HP
\fB\-\-MCMC_samplesN=\fR<MCMC_samplesN>
.IP
Initial number of samples produced. Doubles after every iteration. (default: 1000)
.HP
\fB\-\-MCMC_samplesNmax=\fR<MCMC_samplesNmax>
.IP
Maximum number of samples produced in one iteration. After producing samplesNmax samples sampler finishes. (default: 50000)
.HP
\fB\-\-MCMC_samplesSave=\fR<MCMC_samplesSave>
.IP
Number of samples recorder in total. (default: 1000)
.HP
\fB\-\-MCMC_scaleReduction=\fR<MCMC_scaleReduction>
.IP
Target scale reduction, sampler finishes after this value is met. (default: 1.2)
.HP
\fB\-G\fR ,   \fB\-\-gibbs\fR
.IP
Use Gibbs sampling instead of collapsed Gibbs sampling. (default: Off)
.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, tau). (default: theta)
.HP
\fB\-p\fR <parFileName> ,   \fB\-\-parFile=\fR<parFileName>
.IP
File containing parameters for the sampler, which can be otherwise specified by \fB\-\-MCMC\fR* options. As the file is checked after every MCMC iteration, the parameters can be adjusted while running.
.HP
\fB\-P\fR <procN> ,   \fB\-\-procN=\fR<procN>
.IP
Limit the maximum number of threads to be used. (Default is the number of MCMC chains.)
.HP
\fB\-\-scaleReduction\fR
.IP
Use scale reduction as stopping criterion, instead of computing effective sample size. (default: Off)
.HP
\fB\-s\fR <seed> ,   \fB\-\-seed=\fR<seed>
.IP
Random initialization seed.
.HP
\fB\-\-thetaActFile=\fR<thetaActFileName>
.IP
File for logging noise parameter theta^{act}.
.HP
\fB\-t\fR <trInfoFileName> ,   \fB\-\-trInfoFile=\fR<trInfoFileName>
.IP
File containing transcript information. (Necessary for RPKM)
.HP
\fB\-v\fR ,   \fB\-\-verbose\fR
.IP
Verbose output. (default: Off)