variantCounts: Get variant counts

Description Usage Arguments Value Author(s) Examples

Description

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

Usage

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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

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data("gol_clutch1")

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

CrispRVariants documentation built on Nov. 1, 2018, 2:20 a.m.