Man page - estimateexpression(1)

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Package:  bitseq
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Manual

ESTIMATEEXPRESSION

NAME
SYNOPSIS
DESCRIPTION
OPTIONS

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NAME

estimateExpression - estimate expression given precomputed probabilities of (observed) reads alignments

SYNOPSIS

estimateExpression -o <outFilePrefix> [ OPTIONS ] [ prob file ]

DESCRIPTION

Estimates expression given precomputed probabilities of (observed) reads’ alignments.

Uses MCMC sampling algorithm to produce relative abundance or RPKM.

OPTIONS

--help

Show this help information.

--MCMC_burnIn= <MCMC_burnIn>

Length of sampler’s burn in period. (default: 1000)

--MCMC_chainsN= <MCMC_chainsN>

Number of parallel chains used. At least two chains will be used. (default: 4)

--MCMC_dirAlpha= <MCMC_dirAlpha>

Alpha parameter for the Dirichlet distribution. (default: 1)

--MCMC_samplesDOmax

Produce maximum number of samples (samplesNmax) in second iteration and quit. (default: Off)

--MCMC_samplesN= <MCMC_samplesN>

Initial number of samples produced. Doubles after every iteration. (default: 1000)

--MCMC_samplesNmax= <MCMC_samplesNmax>

Maximum number of samples produced in one iteration. After producing samplesNmax samples sampler finishes. (default: 50000)

--MCMC_samplesSave= <MCMC_samplesSave>

Number of samples recorder in total. (default: 1000)

--MCMC_scaleReduction= <MCMC_scaleReduction>

Target scale reduction, sampler finishes after this value is met. (default: 1.2)

-G , --gibbs

Use Gibbs sampling instead of collapsed Gibbs sampling. (default: Off)

-o <outFilePrefix> , --outPrefix= <outFilePrefix>

Prefix for the output files.

-O <outputType> , --outType= <outputType>

Output type (theta, RPKM, counts, tau). (default: theta)

-p <parFileName> , --parFile= <parFileName>

File containing parameters for the sampler, which can be otherwise specified by --MCMC * options. As the file is checked after every MCMC iteration, the parameters can be adjusted while running.

-P <procN> , --procN= <procN>

Limit the maximum number of threads to be used. (Default is the number of MCMC chains.)

--scaleReduction

Use scale reduction as stopping criterion, instead of computing effective sample size. (default: Off)

-s <seed> , --seed= <seed>

Random initialization seed.

--thetaActFile= <thetaActFileName>

File for logging noise parameter thetaˆ{act}.

-t <trInfoFileName> , --trInfoFile= <trInfoFileName>

File containing transcript information. (Necessary for RPKM)

-v , --verbose

Verbose output. (default: Off)

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