recodeAln: recodeAln

In HLindsay/AlignmentTools: Common operations on GenomicAlignments

Description

Internal AlignmentTools function for recoding an alignment.

Usage

recodeAln(aln, ref = NULL, ref.gap = "+", gap = NULL, nuc = "N",
  nuc.chars = NULL)

Arguments

aln	(DNAStringSet)
ref	(DNAString) the reference sequence (Default: NULL)
ref.gap	(character(1)) Replace locations where the reference sequence has a gap ("-") with ref.gap in alns
gap	(character(1))
nuc	(character(1)) Replace non-gap bases with nuc
nuc.chars	(character(n)) Vector defining characters to replace with "nuc"

Author(s)

Helen Lindsay

Examples

recodeAln(DNAStringSet(c("AA--CC", "AATTC-")), ref = DNAString("AATT--"))

HLindsay/AlignmentTools documentation built on May 8, 2019, 1:36 a.m.