alleleLabelsHelpers: formatVarLabels

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

Description

Internal CrispRVariants function for creating allele labels given variants and positions

Assume that the reference may be on the negative strand and regions are given with respect to the reference sequence.

Usage

.formatVarLabels(grl, labels, position = c("start", "end"),
  genome.to.pos = NULL, pos.to.lab = ":", as.string = TRUE)

.findMismatches(alns, ref.seq, ref.start, regions = NULL, strand = "+",
  min.pct = 0)

Arguments

grl	(GRangesList) A GRangesList of variants. The position of the variants is used in labels
labels	(character(n)) A vector of labels for each variant. In CrispRVariants, this is the size and type of the variant, e.g. "9D" for a 9 bp deletion.
position	One of "start" and "end". Determines whether the start or the end coordinate is used when labeling variants.
genome.to.pos	Optional named vector for transforming variant coordinates into another coordinate system (Default: NULL)
pos.to.lab	(character(1)) Character to join positions and labels (Default: ":", e.g. -3:9D)
as.string	Should individual variant labels be pasted into a single comma separated string when one alignment has multiple variants? (Default: TRUE)
alns	A GAlignments object, where the aligned sequences should span the reference sequence
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.
ref.start	(numeric(1)) The genomic start position of the reference sequence
regions	A GRanges object, regions to check for mismatches with coordinates relative to the reference sequence
strand	One of "+", "-"
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.

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.