label_contigs: label_contigs

In mskilab/loosends: Classifying loose ends in gGraphs

label_contigs

Description

Labels the category of each contig associated with a loose end, as well as the overall category of the loose end. (e.g. T0/T1/T2/MYS)

Usage

label_contigs(
  le,
  bps,
  mapq.gr,
  unmappable.gr,
  mappability.thresh = 0.5,
  specificity.thresh = 0
)

Arguments

bps	(data.table) data.table representing breakpoints coercible to GRanges. bps needs to have columns mapq, tumor.count, and normal.count representing supporting barcodes for that contig.
mapq.gr	(GRanges) tiled granges with field mapq0.frac
unmappable.gr	(GRanges) ranges that are considered CN unmappable
mappability.thresh	(numeric) 0.1 for mappable categorization
specificity.thresh	(numeric) cutoff for tumor-specific contigs
li	(data.table) data.table coercible to GRanges representing loose end
returns	a list with two items: call (data.table with a single row and metadata column call) breakpoints (data.table labeled breakpoints. empty table if no contigs)

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