indelLabels: indelLabels

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

Description

Makes allele labels for insertion / deletion variants

Usage

indelLabels(alns, rc = FALSE, genome.to.pos = NULL, keep.ops = c("I", "D",
  "N"), regions = NULL, ...)

Arguments

alns	(GAligments) aligned reads for finding variants
rc	Should the variants be displayed with respect to the negative strand? (Default: FALSE)
genome.to.pos	A vector with names being genomic locations and values being positions to use in labels (Default: NULL)
keep.ops	CIGAR operations to remain in the variant label (usually indels)
regions	IRanges(k) Regions for counting insertions and deletions. Insertions on the right border are not counted.
...	extra formatting arguments

Value

A vector of labels for alns

Author(s)

Helen Lindsay

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