BitSeq (version 1.16.0)

getExpression: Estimate transcript expression

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

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

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.

See Also

getDE, estimateExpression, parseAlignment