variantCounts {CrispRVariants} | R Documentation

## Get variant counts

### 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)

[Package CrispRVariants version 1.18.0 Index]