score.walks: score.walks

In mskilab/skitools: Various mskilab R utilties

score.walks

Description

Scores GRangesList of walks against GRanges of 10X reads with $BX tag.

Usage

score.walks(
  wks,
  bam = NULL,
  reads = NULL,
  win = NULL,
  wins = NULL,
  use.discordant = FALSE,
  rthresh = 4,
  thresh = 1e+05,
  pad = 10000,
  raw = FALSE,
  allpaths = TRUE,
  verbose = TRUE
)

Arguments

wks	GRangesList of walks
bam	bam file
reads	GRanges of reads with BX tag
win	genomic window in which to score (default is just reduce(unlist(wks))))
wins	tiles to chop up genome further (beyond walk segments)
use.discordant	logical flag whether to process discordant
raw	returns raw barcode by walk matrix of barcode scores

Value

scores of walks or (if raw == tRUE) raw barcode to walk maps

Author(s)

Marcin Imielinski

mskilab/skitools documentation built on Aug. 31, 2023, 1:13 p.m.