ra.merge: Merges rearrangements represented by 'GRangesList' objects

In mskilab/gGnome: gGnome: reference based assembly graph for analyzing rearranged genomes

Merges rearrangements represented by GRangesList objects

Description

Determines overlaps between two or more piles of rearrangement junctions (as named or numbered arguments) +/- padding and will merge those that overlap into single junctions in the output, and then keep track for each output junction which of the input junctions it was "seen in" using logical flag meta data fields prefixed by "seen.by." and then the argument name (or "seen.by.ra" and the argument number)

Usage

ra.merge(..., pad = 0, ignore.strand = FALSE)

Arguments

...	GRangesList representing rearrangements to be merged
pad	non-negative integer specifying padding
ignore.strand	whether to ignore strand (implies all strand information will be ignored, use at your own risk)
ind	logical flag (default FALSE) specifying whether the "seen.by" fields should contain indices of inputs (rather than logical flags) and NA if the given junction is missing

Value

GRangesList of merged junctions with meta data fields specifying which of the inputs each outputted junction was "seen.by"

Examples

# generate some junctions
gr1 <- GRanges(1, IRanges(1:10, width = 1), strand = rep(c('+', '-'), 5))
gr2 <- GRanges(1, IRanges(4 + 1:10, width = 1), strand = rep(c('+', '-'), 5))
ra1 = split(gr1, rep(1:5, each = 2))
ra2 = split(gr2, rep(1:5, each = 2))

ram = ra.merge(ra1, ra2)
values(ram) # shows the metadata with TRUE / FALSE flags

ram2 = ra.merge(ra1, ra2, pad = 5) # more inexact matching results in more merging
values(ram2)

ram3 = ra.merge(ra1, ra2) #indices instead of flags
values(ram3)

mskilab/gGnome documentation built on May 8, 2024, 4:25 p.m.