paChain: paChain

In mskilab/gChain: R Package Providing Additional Capabilities and Speed for GenomicRanges Operations

paChain

Description

Make chain from pairwiseAlignment object

Each BSStringSet must have named sequences (otherwise names will be computed from (perfectly unique) sequences. Each name can only map to a single sequence

NOTE: if XStringSet objects are not provided, then the input is assumed to be DNA (if assume.dna = T), otherwise AA (if assume.dna = F)

Pre-computed pa object can be also provided, but then the sequences from which the pa object was computed should be given as well.

Returns gChain with seqinfos corresponding to unique seqnames in seq1 and seq2 and the interval pairs mapping those two sequences

Usage

paChain(
  seq1,
  seq2,
  sn1 = NULL,
  sn2 = NULL,
  gr1 = NULL,
  gr2 = NULL,
  pa = NULL,
  substitutionMatrix = NULL,
  type = "global",
  verbose = TRUE,
  sl1 = NULL,
  sl2 = NULL,
  score.thresh = NULL,
  both.strands = FALSE,
  keep.best = TRUE,
  assume.dna = TRUE,
  mc.cores = 1,
  mc.chunks = mc.cores,
  pintersect = FALSE,
  ...
)

Author(s)

Marcin Imielinski

mskilab/gChain documentation built on Sept. 28, 2022, 3:45 p.m.