mutationEfficiency {CrispRVariants} | R Documentation

## Get mutation efficiency

### Description

Returns the percentage of sequences that contain at least one mutation.

### Usage

    mutationEfficiency(obj, ...)

    ## S4 method for signature 'CrisprSet'
    mutationEfficiency(obj, ..., snv = c("non_variant",
      "include", "exclude"), include.chimeras = TRUE, exclude.cols = NULL,
      filter.vars = NULL, filter.cols = NULL, group = NULL)

### Arguments

`obj` | An object containing variant counts
`...` | additional arguments
`snv` | Single nucleotide variants (SNVs) may be considered as mutations ("include"), treated as ambiguous sequences and not counted at all ("exclude"), or treated as non-mutations, e.g. sequencing errors or pre-existing SNVs ("non_variant", default)
`include.chimeras` | Should chimeric alignments be counted as variants when calculating mutation efficiency (Default: TRUE
`exclude.cols` | A vector of names of columns in the variant counts table that will not be considered when counting mutation efficiency
`filter.vars` | Variants to remove before calculating efficiency. May be either a variant size, e.g. "1D", or a particular variant/variant combination, e.g. -5:3D
`filter.cols` | A vector of control sample names. Any variants present in the control samples will be counted as non-variant, unless they also contain another indel. Note that this is not compatible with counting snvs as variants.
`group` | A grouping vector. If provided, efficiency will be calculated per group (Default: NULL)

### Value

A vector of efficiency statistics per sample and overall, or a matrix of efficiency statistics per group if a group is provided

### Author(s)

Helen Lindsay

### Examples

    data("gol_clutch1")
    mutationEfficiency(gol)

[Package CrispRVariants version 1.12.0 Index]