mismatchLabels: nonindelLabels

In HLindsay/CrispRVariants: Tools for counting and visualising mutations in a target location

Description

Make variant labels for variants without an insertion or deletion

Usage

mismatchLabels(alns, target, ref.seq, regions = NULL, min.pct = 0,
  mismatch.label = "SNV", genome.to.pos = NULL, as.string = TRUE)

Arguments

alns	A GAlignments object, where the aligned sequences should span the reference sequence
target	(GRanges(1)) The region for counting mismatches
ref.seq	A DNAString object, the sequence for comparison when checking for mismatches. The sequence does not necessarily have to match the mapping reference sequence. Must span all regions if regions are provided.
regions	A GRanges object, regions to check for mismatches with coordinates relative to the reference sequence
min.pct	(numeric(1), between 0 and 100) Only return SNVs that occur at in least min.pct change, not any change at a position.
mismatch.label	(character(1)) Label to append to the start of mismatch strings, if returning as a single string (Default: "SNV:")
genome.to.pos	Optional named vector for transforming variant coordinates into another coordinate system (Default: NULL)
as.string	Should individual variant labels be pasted into a single comma separated string when one alignment has multiple variants? (Default: TRUE)

Value

A data frame of sequence indices, genomic position of mismatch and mismatch base

HLindsay/CrispRVariants documentation built on May 28, 2019, 12:40 p.m.