call_loose_end2: call_loose_end2

In mskilab/loosends: Classifying loose ends in gGraphs

call_loose_end2

Description

labels a single loose end

Usage

call_loose_end2(
  li,
  ri,
  id,
  concat.bwa,
  human.bwa,
  window = 5000,
  low.mappability.gr.fn = system.file("extdata", "wide.multimapping.ranges.rds",
    package = "loosends"),
  unassembled.gr.fn = system.file("extdata", "assembly.gaps.ranges.rds", package =
    "loosends"),
  verbose = FALSE,
  ...
)

Arguments

li	(data.table, GRanges, or character coercible to GRanges)
ri	(reads from loosereads_wrapper)
id	(character) sample id
concat.bwa	(RSeqLib::BWA) reference BWA object with foreign sequences
human.bwa	(RSeqLib::BWA) reference BWA with human only sequences
window	(numeric) window in BP for building contigs, default 5e3
low.mappability.gr.fn	(character) path to low mappability ranges
unassembled.gr.fn	(character) path to low mappability ranges
verbose	(logical) default FALSE
...	(additional inputs to various helper functions)

Value

list with four items

• call

• contigs (curated contigs)

• distal.bps (distal breakends)

• all.bps (all breakends)

• all.tigs (all contigs)

mskilab/loosends documentation built on Aug. 24, 2023, 8:08 a.m.