variantCounts {CrispRVariants} | R Documentation |
Returns a matrix of counts where rows are sequence variants and columns are samples
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)
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) |
A matrix of counts where rows are variants and columns are samples
Helen Lindsay
data("gol_clutch1") #Return a matrix of the 5 most frequent variants variantCounts(gol, top.n = 5)