CrispRVariants (version 1.0.2)

variantCounts: Get variant counts

Description

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

Usage

variantCounts(obj, ...)
"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

Examples

data("gol_clutch1")

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