summarizeQueryRegionsMulti: summarizeQueryRegionsMulti

In BIMSBbioinfo/RCAS: RNA Centric Annotation System

summarizeQueryRegionsMulti

Description

This function is a wrapper function to run RCAS::summarizeQueryRegions multiple times, which is useful to get a matrix of overlap counts between a list of BED files with a txdbFeatures extracted from GTF file

Usage

summarizeQueryRegionsMulti(queryRegionsList, txdbFeatures, nodeN = 1)

Arguments

queryRegionsList	GRangesList object imported from multiple BED files using importBedFiles function
txdbFeatures	List of GRanges objects - outputs of getTxdbFeaturesFromGRanges and getTxdbFeatures functions
nodeN	Positive integer value that denotes the number of cpus to use for parallel processing (default: 1)

Value

A list consisting of two data.frame objects: one for raw overlap counts and one for percentage of overlap counts (raw overlap counts divided by the number of query regions in the corresponding BED file)

Examples

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

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