ssvConsensusIntervalSets: 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

In constrast to ssvOverlapIntervalSets, only regions where a consensus of input grs are present are preserved and annotated.

Usage

ssvConsensusIntervalSets(
  grs,
  ext = 0,
  min_number = 2,
  min_fraction = 0.5,
  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
min_number	An integer number specifying the absloute minimum of input grs that must overlap for a site to be considered consensus.
min_fraction	A numeric between 0 and 1 specifying the fraction of grs that must overlap to be considered consensus.
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.

Details

Only the most stringent of min_number or min_fraction will be applied.

Value

GRanges with metadata columns describing consensus 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))
ssvConsensusIntervalSets(list(a, b))

jrboyd/seqsetvis documentation built on June 1, 2024, 5:39 a.m.