exonExpressionStrandAdjusted: Function that quantifies exon expression based on strand...

In BIMSBbioinfo/reg2gene: Predicting the target genes for regulatory elements

Description

Function that separates stranded and unstranded libraries and quantifies exon expression separately for stranded libraries eg expression of exons located on the + strand is quantified using forward libraries if libraries are unstranded then exon orientations is not taken into account

Usage

exonExpressionStrandAdjusted(exonsForQuant, exonsSplitted, target, sampleIDs,
  libStrand, mc.cores, summaryOperation)

Arguments

target	character, paths to bigwig files
sampleIDs	character, name of samples/bigwig files
libStrand	character, library strandness ("+","-","*")
mc.cores	integer, number of cores for mclapply
summaryOperation	argument for ScoreMatrixBin() how to quantify scores
exons	GRanges object with exon coordinates and metadata about genes
exons.splitted	GRanges object with exon coordinates splitted based on the strand.

Value

Granges object with metadata which corresponds to quantified scores per input exon regions and bigwig files

Author(s)

Inga Patarcic

BIMSBbioinfo/reg2gene documentation built on May 3, 2019, 6:42 p.m.