getExpression: Estimate transcript expression

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

Description

Estimate expression of transcripts. Starting from alignment and reference files function function handles the entire process of expression analysis resulting in transcript expression means and standard deviation together with file containing all the expression samples.

Usage

getExpression(alignFile, trSeqFile, outPrefix=NULL, uniform=TRUE, type="RPKM", 
      log=FALSE, limitA=NULL, seed=NULL, pretend=FALSE, ... )

Arguments

alignFile	File containing read alignments.
trSeqFile	File containing transcript sequence in FASTA format.
outPrefix	Prefix for the output files. Otherwise program creates temporary files, which are only valid for current R session.
uniform	Use uniform read distribution.
type	Output type, possible values: theta, RPKM, counts, tau.
log	Report mean and expression of logged expression samples.
limitA	Limit maximum number of alignments per read. Reads with more alignments than limit will be discarded.
seed	Sets the initial random seed for repeatable experiments.
pretend	Do not execute, only print out command line calls for the C++ version of the program.
...	Other arguments are passed to estimateExpression, please see estimateExpression for more details

Details

This function uses parseAlignment function to compute alignment probabilities and the function estimateExpression to produce the expression samples.

In case of non-uniform read distribution, it first produces approximate estimates of expression using uniform read distribution with VB inference and subsequently uses these estimates to compute read distribution bias-corrected alignment probabilities, which are used in the estimateExpression function to produce expression estimates.

The order of transcripts in the results is always the same as in the alignment file. The transcripts can be identified by names stored in the trInfo part of the result.

Value

list with items:

exp	DataFrame with transcript expression mean and standard deviation
fn	name of the file containing all the expression samples
counts	vector of estimated read counts per transcript
trInfo	DataFrame with transcript information, contains: transcript name, possibly gene name, transcript length, and adjusted transcript length

Author(s)

Peter Glaus

See Also

getDE, estimateExpression, parseAlignment

Examples

## Not run: 
res1 <- getExpression("data-c0b0.sam","ensSelect1.fasta", MCMC_chains=2, 
      MCMC_samplesN=100)

## End(Not run)

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