mutationEfficiency: Get mutation efficiency

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

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)

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