read_support: read_support

In mskilab/loosends: Classifying loose ends in gGraphs

read_support

Description

wrapper around contig.support for easy(-ish) debugging

like contig.support, the input contigs must be nonempty and contain a single qname

Usage

read_support(
  le.dt = data.table(),
  reads.dt = data.table(),
  contigs.dt = data.table(),
  calns = data.table(),
  fasta = "/dev/null",
  ref.bwa = NULL,
  chimeric = TRUE,
  strict = TRUE,
  min.bases = 20,
  min.aligned.frac = 0.95,
  isize.diff = 1000,
  seed.pad = 150,
  all.reads = FALSE,
  bowtie = FALSE,
  outdir = "./",
  verbose = FALSE,
  ...
)

Arguments

le.dt	(data.table) (single row output from process_loose_ends)
reads.dt	(data.table) data.table of reads coercible to GRanges
contigs.dt	(data.table) data.table with colnames track, peak, qname. all qnames should be identical.
calns	(data.table) contig alignments, coercible to GRanges
seed.pad	(numeric) pad around seed for getting supporting reads
all.reads	(logical) return all input reads or just the chunks supporing the contig? (default FALSE)
bowtie	(logical) use bowtie to align reads? if TRUE, fasta must be provided
outdir	(character) output directory for temporary files
verbose	(logical)
...	additional parameters to contig.support

Value

data.table of candidate reads if all.reads is FALSE and there are no supporting reads an empty table is returned if all.reads is TRUE the table will have column $supporting indicating whether read suupports given contig

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