R/AllClasses.R

In adamd3/codondiffR: Codon usage comparisons across taxa

setGeneric(".validity", function(object) standardGeneric(".validity"))


#' S4 class for storing relative codon frequencies in user-supplied sequences.
#'
#' @slot seqID Character vector of sequence identifiers, derived from Fasta
#'    identifier lines.
#' @slot freq Matrix containing the relative frequencies of codons; each
#'    sequence is a row and each codon is a column.
#' @slot ncod Numeric vector of sequence lengths (in codons).
setClass(
    "codonFreq",
    slots = c(
        seqID = "character",
        freq = "matrix",
        ncod = "numeric"
    ),
    prototype = list(
        seqID = NA_character_,
        freq = matrix(nrow = 0, ncol = 0),
        ncod = NA_real_
    ),
    validity= .validity
)