R/AllGenerics.R

In fredcommo/rCGH: Comprehensive Pipeline for Analyzing and Visualizing Array-Based CGH Data

#####################
## ALL GENERICS
#####################

setGeneric("setInfo<-",
    def=function(object, item = NULL, value = NULL)
    standardGeneric("setInfo<-"))
setGeneric("recenter<-",
    def=function(object, value = 0)
    standardGeneric("recenter<-"))
setGeneric("getInfo",
    def=function(object, item = NULL) standardGeneric("getInfo"))
setGeneric("getCNset",
    def=function(object) standardGeneric("getCNset"))
setGeneric("getParam",
    def=function(object) standardGeneric("getParam"))
setGeneric("getSegTable",
    def=function(object, minLen = NULL) standardGeneric("getSegTable"))
setGeneric("adjustSignal",
    def=function(object, Scale = TRUE, Cy = TRUE, GC = TRUE, Ref = "cy3",
    suppOutliers = TRUE, nCores = NULL, verbose = TRUE)
    standardGeneric("adjustSignal"))
setGeneric("segmentCGH",
    def=function(object, Smooth = TRUE, UndoSD = NULL, minLen = 10,
        nCores = NULL, verbose = TRUE) standardGeneric("segmentCGH"))
setGeneric("EMnormalize",
    def=function(object, G=2:6, priorScale=5, peakThresh=0.5, mergeVal=0.1,
            Title=NA, verbose=TRUE) standardGeneric("EMnormalize"))
setGeneric("plotDensity",
    def=function(object, breaks = NULL, Title = NULL,...)
    standardGeneric("plotDensity"))
setGeneric("plotProfile",
    def=function(object, showCopy = FALSE, symbol = NULL,
        gain = .5, loss = (-.5), minLen = 10,
        pCol = "grey50", GLcol = c("blue", "red3"), Title = NULL, ylim = NULL)
    standardGeneric("plotProfile")
    )
setGeneric("plotLOH",
    def=function(object, Title = NULL) standardGeneric("plotLOH"))
setGeneric("multiplot",
    def=function(object, symbol = NULL, gain = .5,
        loss = (-.5), minLen = 10,
        pCol = "grey50", GLcol = c("blue", "red3"),
        L = matrix(seq(1, 12)),
        p = c(1/2, 1/4, 1/4), Title = NULL, ylim = NULL)
    standardGeneric("multiplot")
    )
setGeneric("view",
    def=function(object, browser = TRUE, ...) standardGeneric("view"))