summarizeQueryRegionsMulti {RCAS} | R Documentation |
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
summarizeQueryRegionsMulti(queryRegionsList, txdbFeatures, nodeN = 1)
queryRegionsList |
GRangesList object imported from multiple BED files
using |
txdbFeatures |
List of GRanges objects - outputs of
|
nodeN |
Positive integer value that denotes the number of cpus to use for parallel processing (default: 1) |
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)
data(gff) data(queryRegions) queryRegionsList <- GRangesList(queryRegions, queryRegions) names(queryRegionsList) <- c('q1', 'q2') txdbFeatures <- getTxdbFeaturesFromGRanges(gffData = gff) summaryMatrix <- summarizeQueryRegionsMulti(queryRegionsList = queryRegionsList, txdbFeatures = txdbFeatures)