check_contig_concordance: check_contig_concordance

In mskilab/loosends: Classifying loose ends in gGraphs

check_contig_concordance

Description

check_contig_concordance

Usage

check_contig_concordance(calns, verbose = FALSE)

Arguments

calns	(data.table of contig alignments) needs to have columns "tumor.specific" and "tumor.support"
verbose	(logical) default FALSE

Value

data.table with one row with the following columns

• any.alt (logical)

• somatic.alt (logical)

• junction (logical) are any of the contigs high-mapq junctions?

• complex (logical) are any of the contigs high-mapq phased complex rearrangements (no junctions)?

• single breakend (logical) no high-mapq junctions or phased complex rearrangements, but there are ALT contigs.

• insertion (logical) do the junctions contain insertions? (NA if not a junction)

• homology (logical) do the junctions contain nonzero breakend homology? (NA if not a junction)

• telomeric (logical) do any tumor-specific contigs contain telomeric sequence?

• jstring (character) grl of the consensus junction (NA if not a junctions)

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