summarizeQueryRegionsMulti {RCAS} | R Documentation

## 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)

[Package RCAS version 1.16.0 Index]