cocount: cocount

In mskilab/GxG: GxG: Genomic matrices and pairwise genomic features based on GenomicRanges and data.table

cocount

Description

gMatrix instantiator creates contact "counts" of "events", which are GRanges grouped into pairs / triples / groups (e.g. paired end reads, linked readsa, SPRITE contacts) via "by" column.

Usage

cocount(
  events,
  bins = disjoin(events),
  by = names(values(events))[1],
  weight = NULL,
  frac = FALSE,
  full = FALSE,
  fill = 0,
  na.rm = TRUE
)

Arguments

events	GRanges of events
bins	bins to count to, default is disjoin(events)
by	column of events GRanges that allows co-counting
frac	whether to count fractional overlap of event with bin as 1 (frac == FALSE) or based on width

mskilab/GxG documentation built on April 12, 2025, 5:32 p.m.