variantCounts: Get variant counts

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

Description

Returns a matrix of counts where rows are sequence variants and columns are samples

Usage

variantCounts(obj, ...)

## S4 method for signature 'CrisprSet'
variantCounts(obj, ..., top.n = NULL, min.freq = 0,
  min.count = 1, include.chimeras = TRUE, include.nonindel = TRUE,
  result = "counts", filter.vars = NULL)

Arguments

obj	An object containing variant counts
...	Additional arguments
top.n	(Integer n) If specified, return variants ranked at least n according to frequency across all samples (Default: 0, i.e. no cutoff)
min.freq	(Float n least one sample (Default: 0)
min.count	(Integer n) Return variants with count greater than n in at least one sample (Default: 0)
include.chimeras	Should chimeric reads be included in the counts table? (Default: TRUE)
include.nonindel	Should sequences without indels be returned? (Default:TRUE)
result	Return variants as either counts ("counts", default) or proportions ("proportions")
filter.vars	Labels of variants alleles to remove (Default: NULL)

Value

A matrix of counts where rows are variants and columns are samples

Author(s)

Helen Lindsay

Examples

data("gol_clutch1")

#Return a matrix of the 5 most frequent variants
variantCounts(gol, top.n = 5)

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