getFeatureBoundaryCoverageMulti: getFeatureBoundaryCoverageMulti

Description Usage Arguments Value Examples

View source: R/meta_analysis_functions.R

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

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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

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

RCAS documentation built on April 29, 2020, 5:38 a.m.