getFeatureBoundaryCoverageMulti {RCAS} | R Documentation

## getFeatureBoundaryCoverageMulti

### 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

    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

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

[Package RCAS version 1.4.4 Index]