Annotate IGH Breakpoints. — annotate_igh

Add annotation to IGH breakpoints to infer mechanism based on location within IGH.

annotate_igh_breakpoints(annotated_df, genome_build = "grch37")

Arguments

annotated_df: Previously annotated data frame of SVs.
genome_build: Version of reference build to be used, only grch37 currently accepted.

Value

A slightly modified bedpe with added columns.

Details

Returns a modified bedpe with additional columns. The most useful columns that are added are mechanism (one of CSR, AID, VDJ) and label (NA if unmatched, otherwise one of Emu, Smu, one of the J segments or switch regions).

Examples

manta_sv = get_manta_sv(verbose = FALSE)
#> WARNING! No SV calls found in flat-file for: 171116-PL02
#> WARNING! No SV calls found in flat-file for: 171447-PL01
#> WARNING! No SV calls found in flat-file for: 171451-PL01
all_annotated = annotate_sv(sv_data = manta_sv)
ig_annotated = annotate_igh_breakpoints(all_annotated)