ra.overlaps: ra.overlaps

In mskilab/gUtils: R Package Providing Additional Capabilities and Speed for GenomicRanges Operations

ra.overlaps

Description

Determines overlaps between two piles of rearrangement junctions ra1 and ra2 (each GRangesLists of signed locus pairs) against each other, returning a sparseMatrix that is T at entry ij if junction i overlaps junction j.

if argument pad = 0 (default) then only perfect overlap will validate, otherwise if pad>0 is given, then padded overlap is allowed

strand matters, though we test overlap of both ra1[i] vs ra2[j] and gr.flipstrand(ra2[j])

Usage

ra.overlaps(ra1, ra2, pad = 0, arr.ind = TRUE, ignore.strand = FALSE, ...)

Arguments

ra1	GRangesList with rearrangement set 1
ra2	GRangesList with rearrangement set 2
pad	Amount to pad the overlaps by. Larger is more permissive. Default is exact (0)
arr.ind	Default TRUE
ignore.strand	Ignore rearrangement orientation when doing overlaps. Default FALSE
...	params to be sent to gr.findoverlaps

mskilab/gUtils documentation built on June 6, 2023, 12:08 a.m.