getFeatureBoundaryCoverage: getFeatureBoundaryCoverage

In RCAS: RNA Centric Annotation System

Description

This function extracts the flanking regions of 5' and 3' boundaries of a given set of genomic features and computes the per-base coverage of query regions across these boundaries.

Usage

getFeatureBoundaryCoverage(
  queryRegions,
  featureCoords,
  flankSize = 500,
  boundaryType,
  sampleN = 0
)

Arguments

queryRegions	GRanges object imported from a BED file using importBed function
featureCoords	GRanges object containing the target feature coordinates
flankSize	Positive integer that determines the number of base pairs to extract around a given genomic feature boundary
boundaryType	(Options: fiveprime or threeprime). Denotes which side of the feature's boundary is to be profiled.
sampleN	A positive integer value less than the total number of featuer coordinates that determines whether the target feature coordinates should be randomly downsampled. If set to 0, no downsampling will happen. If

Value

a data frame containin three columns. 1. fivePrime: Coverage at 5' end of features 2. threePrime: Coverage at 3' end of features; 3. bases: distance (in bp) to the boundary

Examples

data(queryRegions)
data(gff)
txdb <- GenomicFeatures::makeTxDbFromGRanges(gff)
transcriptCoords <- GenomicFeatures::transcripts(txdb)
transcriptEndCoverage <- getFeatureBoundaryCoverage (
                                     queryRegions = queryRegions,
                                    featureCoords = transcriptCoords,
                                    flankSize = 100,
                                    boundaryType = 'threeprime',
                                    sampleN = 1000)

RCAS documentation built on Nov. 8, 2020, 8:03 p.m.