mutationEfficiency {CrispRVariants} | R Documentation |
Returns the percentage of sequences that contain at least one mutation.
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)
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) |
A vector of efficiency statistics per sample and overall, or a matrix of efficiency statistics per group if a group is provided
Helen Lindsay
data("gol_clutch1") mutationEfficiency(gol)