calcPairwiseAlignment: Helper function to calculate the optimal pairwise alignment...

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

Helper function to calculate the optimal pairwise alignment of a fusion of type, 'mechanism'.

Description

Returns a data.table for the fusion with the best scoring alignment (or no alignment) for each repair pathway.

Usage

calcPairwiseAlignment(
  DT,
  bsg,
  mechanism = c("NHEJ", "SSA", "MMEJ", "BIR", "MMBIR"),
  window = 4,
  gapOpening = Inf,
  gapExtension = Inf,
  ...
)

Arguments

DT	A data.table object containing fusion predictions.
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.

Value

A data.table object with identified homologies.

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