queryGff {RCAS} | R Documentation

## queryGff

### Description

This function checks overlaps between the regions in input query and in reference. Input query should be in BED format and reference should be in GFF format. Both data are imported as GRanges object.

### Usage

    queryGff(queryRegions, gffData)

### Arguments

`queryRegions` | GRanges object imported from a BED file using `importBed` function
`gffData` | GRanges object imported from a GTF file using `importGtf` function

### Value

a GRanges object (a subset of input gff) with an additional column 'overlappingQuery' that contains the coordinates of query regions that overlap the target annotation features

### Examples

    data(queryRegions)
    data(gff)
    overlaps <- queryGff(queryRegions = queryRegions, gffData = gff)

[Package RCAS version 1.12.0 Index]