estimateVBExpression: Estimate expression of transcripts using VB

In BitSeq: Transcript expression inference and differential expression analysis for RNA-seq data

Description

Estimates the expression of transcripts using Variational Bayes inference algorithm

Usage

estimateVBExpression (probFile, outFile, outputType=NULL, trInfoFile=NULL, 
      seed=NULL, samples=NULL, optLimit=1e-5, optMethod="FR", procN=4, 
      verbose=FALSE, veryVerbose=FALSE, pretend=FALSE)

Arguments

probFile	File with alignment probabilities produced by parseAlignment
outFile	Prefix for the output files.
outputType	Output type, possible values: theta, RPKM, counts. This is only relevant when the samples option is used. Default: theta.
trInfoFile	File containing transcript information. (Necessary for RPKM output)
seed	Sets the initial random seed for repeatable experiments.
samples	Number of samples to be generated from the posterior distribution. Default: no samples are generated.
verbose	Verbose output.
veryVerbose	Very verbose output.
procN	Maximum number of threads to be used. The program will not use more threads that there are MCMC chains.

Advanced options:

optLimit	The optimisation limit in terms of minimal gradient or change of bound.
optMethod	The optimisation method, use "FR", "HR", or "steepest".
pretend	Do not execute, only print out command line calls for the C++ version of the program.

Details

This function runs Variational Bayes algorithm to estimate the transcript expression. The input is the .prob file containing alignment probabilities which were produced by parseAlignment. Other optional input is the transcript information file specified by trInfoFile and again produced by parseAlignment.

It is much faster inference than MCMC which estimates mean expression equally well. However, the posterior is in form of Dirichlet distribution with underestimated variance. Use this method in cases when you are only interested in mean expression.

Value

.m_alphas

file containing mean relative expression of transcripts theta and parameters of the Dirichlet distribution. Please note the first line in the file corresponds to the noise transcript.

If option samples is used, the program also generates samples based of the outputType, the default would be file with extension ".VBtheta".

Author(s)

Peter Glaus

See Also

parseAlignment, estimateExpression

Examples

## Not run: 
setwd(system.file("extdata",package="BitSeq"))
parseAlignment( "data-c0b0.sam", outFile = "data-c0b0.prob", trSeqFile = "ensSelect1.fasta",
      trInfoFile = "data.tr", uniform = TRUE);

estimateVBExpression( probFile="data-c0b0.prob", outFile="data-c0b0-a", outputType="RPKM", 
      samples=1000, trInfoFile="data.tr", seed=47, verbose=TRUE)
estimateVBExpression( probFile="data-c0b0.prob", outFile="data-c0b0-b", trInfoFile="data.tr")
estimateVBExpression( probFile="data-c0b0.prob", outFile="data-c0b0-c", trInfoFile="data.tr", 
      optLimit=1e-6, optMethod = "HS", procN=12, veryVerbose=TRUE);

## End(Not run)

BitSeq documentation built on Nov. 8, 2020, 5:25 p.m.