getFeatureBoundaryCoverageMulti: getFeatureBoundaryCoverageMulti

In BIMSBbioinfo/RCAS: RNA Centric Annotation System

getFeatureBoundaryCoverageMulti

Description

This function is a wrapper function to run RCAS::getFeatureBoundaryCoverage multiple times, which is useful to get coverage signals across different kinds of transcript features for a given list of bed files imported as a GRangesList object.

Usage

getFeatureBoundaryCoverageMulti(bedData, txdbFeatures, sampleN = 10000)

Arguments

bedData	GRangesList object imported from multiple BED files using importBedFiles function
txdbFeatures	List of GRanges objects - outputs of getTxdbFeaturesFromGRanges and getTxdbFeatures functions
sampleN	(default=10000) Positive integer value that is used to randomly down-sample the target feature coordinates to improve the runtime. Set to 0 to avoid downsampling.

Value

A data.frame object with coverage data at three prime and five prime boundaries of a list of transcript features

Examples

data(gff)
data(queryRegions)
queryRegionsList <- GenomicRanges::GRangesList(queryRegions, queryRegions)
names(queryRegionsList) <- c('q1', 'q2')
txdbFeatures <- getTxdbFeaturesFromGRanges(gffData = gff)
getFeatureBoundaryCoverageMulti(queryRegionsList, txdbFeatures, sampleN = 500)

BIMSBbioinfo/RCAS documentation built on Feb. 7, 2024, 4:38 p.m.