find_overlaps: Find overlapping indices of two gtf/gff/bed/bam objects

In openanalytics/gcount: Obtain Raw Read Counts from RNASeq Data

Description

For internal use only. Function for finding overlaps between two objects of class gtf/gff/bed/bam using GenomicRanges::findOverlaps.

Usage

find_overlaps(x, y, ignore_redundant = FALSE, ignore_strand = FALSE, ...)

Arguments

x, y	An object of class gtf, gff, bed or bam.
ignore_redundant	Should redundant overlaps be ignored?
ignore_strand	Logical argument to pass to GRanges function. Indicates whether strand should be ignored when constructing GRanges object or not. Default is FALSE.
...	Additional arguments passed to GenomicRanges::findOverlaps.

Value

A data.table containing overlapping indices.

openanalytics/gcount documentation built on May 24, 2019, 2:26 p.m.