summarizeQueryRegionsMulti: summarizeQueryRegionsMulti

Description Usage Arguments Value Examples

View source: R/meta_analysis_functions.R

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

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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

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

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