calcNHEJ: Helper function to calculate NHEJ homologies

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

Helper function to calculate NHEJ homologies

Description

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

Usage

calcNHEJ(DT, bsg, window = 4, gapOpening = Inf, gapExtension = 4, ...)

Arguments

DT	A data.table object containing fusion predictions.
bsg	A BSgenome string or BSgenome object.
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 putative homologies.

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