ssvOverlapIntervalSets: Intersect a list of GRanges to create a single GRanges object...

In jrboyd/seqsetvis: Set Based Visualizations for Next-Gen Sequencing Data

Intersect a list of GRanges to create a single GRanges object of merged ranges including metadata describing overlaps per input GRanges

Description

Intersect a list of GRanges to create a single GRanges object of merged ranges including metadata describing overlaps per input GRanges

Usage

ssvOverlapIntervalSets(
  grs,
  ext = 0,
  use_first = FALSE,
  preserve_mcols = FALSE,
  ...
)

Arguments

grs	A list of GRanges
ext	An integer specifying how far to extend ranges before merging. in effect, ranges withing 2*ext of one another will be joined during the merge
use_first	A logical. If True, instead of merging all grs, only use first and add metadata logicals for others.
preserve_mcols	Controls carrying forward mcols metadata from input list of GRanges. If TRUE, all mcols will be carried forward with the item name appended. If a character vector, only those attributes will be carried and all must be present in all GRanges. The default of FALSE will carry nothing forward and only membership table will be generated. ssvAnnotateSubjectGRanges is used internally.
...	arguments passed to IRanges::findOverlaps, i.e. maxgap, minoverlap, type, select, invert.

Value

GRanges with metadata columns describing overlap of input grs.

Examples

library(GenomicRanges)
a = GRanges("chr1", IRanges(1:7*10, 1:7*10))
b = GRanges("chr1", IRanges(5:10*10, 5:10*10))
ssvOverlapIntervalSets(list(a, b))

jrboyd/seqsetvis documentation built on Oct. 15, 2024, 11:28 p.m.