queryGff: queryGff

In RCAS: RNA Centric Annotation System

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)

RCAS documentation built on Nov. 8, 2020, 8:03 p.m.