check_contig_support_wrapper: check_contig_support_wrapper

In mskilab/loosends: Classifying loose ends in gGraphs

check_contig_support_wrapper

Description

Given a set of filtered contigs, checks support for each contig using the appropriate function e.g. if the contig is chimeric, uses check_split_contig_support whereas, if the contig contains the distal side only, uses check_distal_only_contig_support

Produces a data table with the name of each contig and the number of tumor/normal supporting qnames

Usage

check_contig_support_wrapper(
  calns,
  reads.dt,
  ref,
  name.field = "name",
  min.supp.reads = 2,
  max.normal.reads = 10,
  min.read.ratio = 10,
  verbose = FALSE
)

Arguments

calns	(data.table) alignment for POSSIBLY MULTIPLE contigs
reads.dt	(data.table)
ref	(BWA)
name.field	(character) default "name"
min.supp.reads	(numeric) min number of supporting reads to be considered as having read support (default 2)
max.normal.reads	(numeric) maximum accepted number of supporting reads in normal (default 5)
min.read.ratio	(numeric) minimum ratio of tumor to normal reads (default 5)
verbose	(logical) default FALSE

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