calcHomology: Checks a fusion for hallmarks of microhomology error prone...

In databio/FUSED: FUSED: FUSion Error prone repair Detection

Checks a fusion for hallmarks of microhomology error prone repairs. Returns a data.table for the fusion with the best scoring alignment (or no alignment) for each repair pathway.

Description

Checks a fusion for hallmarks of microhomology error prone repairs. Returns a data.table for the fusion with the best scoring alignment (or no alignment) for each repair pathway.

Usage

calcHomology(
  DT,
  bsg,
  mechanism = c("ALL", "NHEJ", "SSA", "MMEJ", "BIR", "MMBIR"),
  window = NA,
  gapOpening = NA,
  gapExtension = NA,
  source = c("STAR", "ARRIBA", "ORIEN"),
  ...
)

Arguments

DT	A data.table object representing a single fusion.
bsg	A BSgenome string or BSgenome object.
mechanism	A character vector representing which repair pathway to investigate in the given fusion data.table.
window	A numeric value representing how upstream and downstream of a fusion breakpoint within which to perform sequence alignment.
gapOpening	A numeric value representing the cost for opening a gap in the alignment.
gapExtension	A numeric value representing the incremental cost for extending the gap in alignment.
source	A character vector representing the fusion prediction source.

Value

A data.table object with fusion alignments for specified mechanism.

databio/FUSED documentation built on May 13, 2022, 8:10 p.m.