# SeqData - AllGenerics
#
#
###############################################################################
# Generics for Methods
##' @exportMethod viewCoverage
setGeneric(
name="viewCoverage",
def=function(obj=NULL,obj.control=NULL, bamFile=character(0),bamFile.control=character(0),weight.control=1,feature=character(0),ranges=GRanges(),annotationFile=character(0),split.metaData=F,bigWig=F,smooth=T,description=character(0)){
standardGeneric("viewCoverage")
})
##' @exportMethod getReadCoverage
setGeneric(
name="getReadCoverage",
def=function(obj,bamFile=character(0)){
standardGeneric("getReadCoverage")
})
##' @exportMethod getReadAlignment
setGeneric(
name="getReadAlignment",
def=function(obj,bamFile=character(0),annotationFile=character(0)){
standardGeneric("getReadAlignment")
})
##' @exportMethod getFeatureAnnotation
setGeneric(
name="getFeatureAnnotation",
def=function(obj=NULL,annotationFile=character(0),feature="gene"){
standardGeneric("getFeatureAnnotation")
})
##' @exportMethod countReads
setGeneric(
name="countReads",
def=function(obj=NULL,bamFile=character(0),annotationFile=character(0),countingMode="Union",interFeature=TRUE,feature=character(0),description=character(0)){
standardGeneric("countReads")
})
##' @exportMethod findPeaks
setGeneric(
name="findPeaks",
def=function(obj.chip=NULL,obj.control=NULL,bamFile.chip=character(0),bamFile.control=character(0),fdr.max=1e-5,foldChange.min=2,description=character(0),local.lambda=T){
standardGeneric("findPeaks")
})
##' @exportMethod getBaseAlignment
setGeneric(
name="getBaseAlignment",
def=function(obj=NULL,bamFile=character(0),baseReport=character(0)){
standardGeneric("getBaseAlignment")
})
##' @exportMethod summarizeBases
setGeneric(
name="summarizeBases",
def=function(obj=NULL,bamFile=character(0),annotationFile=character(0),baseReport=charcter(0),description=character(0)){
standardGeneric("summarizeBases")
})
##' @exportMethod getBaseScore
setGeneric(
name="getBaseScore",
def=function(obj=NULL,bamFile=character(0),baseReport=charcter(0),FUN=.perc,output="coverage"){
standardGeneric("getBaseScore")
})
##------------------------------------------------------------------------------
# Generics for Accessors and Setters
##'@exportMethod chrSize<-
setGeneric(
name="chrSize<-",
def=function(obj,value){
standardGeneric("chrSize<-")
})
##'@exportMethod chrSize
setGeneric(
name="chrSize",
def=function(obj){
standardGeneric("chrSize")
})
##' @exportMethod libSize<-
setGeneric(
name="libSize<-",
def=function(obj,value){
standardGeneric("libSize<-")
})
##' @exportMethod libSize
setGeneric(
name="libSize",
def=function(obj){
standardGeneric("libSize")
})
##' @exportMethod readAlignment<-
setGeneric(
name="readAlignment<-",
def=function(obj,value){
standardGeneric("readAlignment<-")
})
##' @exportMethod readAlignment
setGeneric(
name="readAlignment",
def=function(obj){
standardGeneric("readAlignment")
})
##' @exportMethod readCoverage
setGeneric(
name="readCoverage",
def=function(obj){
standardGeneric("readCoverage")
})
##' @exportMethod readCoverage<-
setGeneric(
name="readCoverage<-",
def=function(obj,value){
standardGeneric("readCoverage<-")
})
##' @exportMethod featureAnnotation<-
setGeneric(
name="featureAnnotation<-",
def=function(obj,value){
standardGeneric("featureAnnotation<-")
})
##' @exportMethod featureAnnotation
setGeneric(
name="featureAnnotation",
def=function(obj){
standardGeneric("featureAnnotation")
})
##' @exportMethod coverageView
setGeneric(
name="coverageView",
def=function(obj){
standardGeneric("coverageView")
})
##' @exportMethod coverageView<-
setGeneric(
name="coverageView<-",
def=function(obj,value){
standardGeneric("coverageView<-")
})
##' @exportMethod annotatePeaks
setGeneric(
name="annotatePeaks",
def=function(obj=NULL,peakTable=character(0),annotationFile=character(0),feature=character(0),distance.max=4000,description=character(0)){
standardGeneric("annotatePeaks")
})
##' @exportMethod bamFile
setGeneric(
name="bamFile",
def=function(obj){
standardGeneric("bamFile")
})
##' @exportMethod bamFile<-
setGeneric(
name="bamFile<-",
def=function(obj,value){
standardGeneric("bamFile<-")
})
##' @exportMethod annotationFile
setGeneric(
name="annotationFile",
def=function(obj){
standardGeneric("annotationFile")
})
##' @exportMethod annotationFile<-
setGeneric(
name="annotationFile<-",
def=function(obj,value){
standardGeneric("annotationFile<-")
})
##' @exportMethod coverageView
setGeneric(
name="coverageView",
def=function(obj,ranges){
standardGeneric("coverageView")
})
##' @exportMethod intersectChr
setGeneric(
name="intersectChr",
def=function(reads,features){
standardGeneric("intersectChr")
})
##' @exportMethod baseAlignment<-
setGeneric(
name="baseAlignment<-",
def=function(obj,value){
standardGeneric("baseAlignment<-")
})
##' @exportMethod baseAlignment
setGeneric(
name="baseAlignment",
def=function(obj){
standardGeneric("baseAlignment")
})
##' @exportMethod baseScore<-
setGeneric(
name="baseScore<-",
def=function(obj,value){
standardGeneric("baseScore<-")
})
##' @exportMethod baseScore
setGeneric(
name="baseScore",
def=function(obj){
standardGeneric("baseScore")
})
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