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 theta^{act}.
-t <trInfoFileName> , --trInfoFile=<trInfoFileName>
-
File containing transcript information. (Necessary for RPKM)
-v , --verbose
-
Verbose output. (default: Off)