R/AllGenerics.R

In rformassspectrometry/QFeatures: Quantitative features for mass spectrometry data

##' @title Placeholder for generics functions documentation
##'
##' @name AllGenerics
##' @rdname AllGenerics
NULL

setGeneric("readQFeatures",
           function(assayData, colAnnotation, ...)
               standardGeneric("readQFeatures"))

setGeneric("subsetByFeature",
           function(x, y, ...) standardGeneric("subsetByFeature"))

setGeneric("zeroIsNA",
           function(object, i) standardGeneric("zeroIsNA"))

setGeneric("infIsNA",
           function(object, i) standardGeneric("infIsNA"))

setGeneric("nNA",
           function(object, i) standardGeneric("nNA"))

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

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

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

## base::sweep
.sweep.useAsDefault <- function(x, MARGIN, STATS, FUN = "-",
                                check.margin = TRUE, ...)
    base::sweep(x, MARGIN, STATS, FUN, check.margin, ...)

setGeneric("sweep",
           signature = "x",
           function(x, MARGIN, STATS, FUN = "-", check.margin = TRUE, ...)
               standardGeneric("sweep"),
           useAsDefault = .sweep.useAsDefault)