R/methods-gSetList.R

In benilton/oligoClasses-release: Classes for high-throughput arrays supported by oligo and crlmm

setMethod("initialize", signature(.Object="gSetList"),
	  function(.Object,
		   assayDataList=AssayDataList(...),
		   featureDataList=GenomeAnnotatedDataFrameFromList(assayDataList),
		   chromosome=integer(),
		   phenoData=annotatedDataFrameFrom(assayDataList, byrow=FALSE),
		   protocolData=phenoData[, integer(0)],
		   experimentData=new("MIAME"),
		   annotation=character(),
		   genome=character(),
		   ...){
		  callNextMethod(.Object,
				 assayDataList=assayDataList,
				 featureDataList=featureDataList,
				 phenoData=phenoData,
				 chromosome=chromosome,
				 annotation=annotation,
				 genome=genome,
				 protocolData=protocolData,
				 experimentData=experimentData,
				 ...)
	  })

setMethod("[", signature(x="gSetList"),
	  function(x, i, j, ..., drop=FALSE){
		  ## using 'i' to subset markers does not really make
		  ## sense
		  ##
		  ## Use i to subset the list. example, x[1] is still a BeadStudioSetList, but is one chromosome
		  ##
		  if(!missing(i) & !missing(j)){
			  ##browser()
			  ad <- assayDataList(x)
			  nms <- ls(ad)
			  for(k in seq_along(nms)){
				  elt <- nms[k]
				  tmp <- ad[[elt]][i]
				  tmp <- lapply(tmp, function(x, j) {
					  x[, j, drop=FALSE]
				  }, j=j)
				  x <- assayDataElementReplace(x, elt, tmp)
			  }
			  x@chromosome <- chromosome(x)[i]
			  x@featureDataList <- featureDataList(x)[i]
			  x@phenoData <- phenoData(x)[j, ]
		  }
		  if(!missing(i) & missing(j)){
			  ad <- assayDataList(x)
			  nms <- ls(ad)
			  for(k in seq_along(nms)){
				  elt <- nms[k]
				  tmp <- ad[[elt]][i]
				  x <- assayDataElementReplace(x, elt, tmp)
			  }
			  x@chromosome <- chromosome(x)[i]
			  x@featureDataList <- featureDataList(x)[i]
		  }
		  if(missing(i) & !missing(j)){
			  ad <- assayDataList(x)
			  nms <- ls(ad)
			  for(k in seq_along(nms)){
				  elt <- nms[k]
				  tmp <- lapply(ad[[elt]], function(x, j) {
					  x[, j, drop=FALSE]
				  }, j=j)
				  x <- assayDataElementReplace(x, elt, tmp)
			  }
			  x@phenoData <- phenoData(x)[j, ]
		  }
		  return(x)
	  })

setAs("gSetList", "list", function(from){
	to <- vector("list", length(from))
	for(i in seq_along(from)){
		to[[i]] <- from[[i]]
	}
	return(to)
})

setMethod("$", signature(x="gSetList"),
	  function(x, name){
            eval(substitute(phenoData(x)$NAME_ARG, list(NAME_ARG=name)))
	  })

setReplaceMethod("$", "gSetList", function(x, name, value) {
	phenoData(x)[[name]] = value
	x
})

setMethod("annotation", signature(object="gSetList"), function(object) object@annotation)


setMethod("assayData", signature(object="gSetList"),
	  function(object) assayDataList(object))

setMethod("assayDataList", signature(object="gSetList"),
	  function(object)  object@assayDataList)

setMethod("assayDataList", signature(object="oligoSetList"),
	  function(object)  object@assayDataList)

setMethod("chromosome", signature(object="gSetList"),
	  function(object, as.list=FALSE, ...){
		  ##lapply(object, chromosome)
		  if(!as.list) object@chromosome else chromosomeList(object)
	  })

setMethod("dims", signature(object="gSetList"), function(object){
	nchr <- length(chromosome(object))
	nr <- sum(elementLengths(object))
	ns <- ncol(object)
	ds <- c(nr, nchr, ns)
	names(ds) <- c("features (total)", "list elements", "samples")
	return(ds)
})

setReplaceMethod("featureData", signature(object="gSetList", value="list"),
		 function(object, value){
			 object@featureDataList <- value
			 object
		 })

setMethod("featureData", signature(object="gSetList"),
		 function(object){
			 object@featureDataList
		 })

setMethod("fvarLabels", signature(object="gSetList"),
	  function(object){
		  varLabels(featureData(object)[[1]])
	  })

setMethod("featureDataList", signature(object="gSetList"),
	  function(object)  object@featureDataList)

setMethod("featureNames", signature(object="gSetList"),
	  function(object){
		  lapply(featureDataList(object), featureNames)
	  })

setMethod("genomeBuild", signature(object="gSetList"), function(object) object@genome)
setReplaceMethod("genomeBuild", signature(object="gSetList", value="character"), function(object, value){
	object@genome <- value
	object
})

setMethod("length", signature(x="gSetList"), function(x) length(x@chromosome))

setMethod("order", signature(...="gSetList"),
	  function(..., na.last=TRUE,decreasing=FALSE){
		  x <- list(...)[[1]]
		  for(i in seq_along(x)){
			  x[[i]] <- chromosomePositionOrder(x[[i]])
		  }
		  return(x)
	  })

setMethod("pData", signature(object="gSetList"),
	  function(object) pData(phenoData(object)))

setMethod("phenoData", signature(object="gSetList"),
	  function(object) object@phenoData)

setReplaceMethod("phenoData",
                 signature=signature(
		 object="gSetList",
                   value="AnnotatedDataFrame"),
                 function(object, value) {
			 object@phenoData <- value
			 object
                 })

setReplaceMethod("pData",
                 signature=signature(
		 object="gSetList",
                   value="data.frame"),
                 function(object, value) {
			 pd <- phenoData(object)
			 pData(pd) <- value
			 phenoData(object) <- pd
			 object
                 })

setMethod("position", signature(object="gSetList"),
	  function(object){
		  lapply(featureDataList(object), position)
	  })

setMethod("sampleNames", signature(object="gSetList"),
	  function(object) sampleNames(phenoData(object)))

setReplaceMethod("sampleNames", signature(object="gSetList", value="character"),
		 function(object,value){
			 sampleNamesGSetList(object, value)
		 })

sampleNamesGSetList <- function(object, value){
	pd <- phenoData(object)
	sampleNames(pd) <- value
	object@phenoData <- pd
	adl <- object@assayDataList
	lrrlist <- adl[["lrr"]]
	baflist <- adl[["baf"]]
	relabel <- function(object, names){
		colnames(object) <- names
		object
	}
	if(length(lrrlist) > 0){
		lrrlist <- lapply(lrrlist, relabel, names=value)
		baflist <- lapply(baflist, relabel, names=value)
	}
	assayData <- new.env(parent=emptyenv())
	assayData[["lrr"]] <- lrrlist
	assayData[["baf"]] <- baflist
	##	adl[["lrr"]] <- lrrlist
	##	adl[["baf"]] <- baflist
	object@assayDataList <- assayData
	return(object)
}

setMethod("sapply", signature(X="gSetList"),
	  function(X, FUN, ..., simplify=TRUE, USE.NAMES=TRUE){
		  listobject <- as(X, "list")
		  sapply(listobject, FUN, ..., simplify=simplify, USE.NAMES=USE.NAMES)
	  })

setMethod("show", signature(object="gSetList"),
	  function(object){
		  nm <- ls(assayData(object))[[1]]
		  lo <- length(assayData(object)[[nm]])
		  cat(class(object), " of length ", lo, "\n", sep="")
	  })

setMethod("storageMode", "gSetList", function(object) storageMode(assayData(object)))

setMethod("varLabels", signature(object="gSetList"),
	  function(object) varLabels(phenoData(object)))

setMethod("makeFeatureGRanges", signature(object="gSetList"),
	  function(object, ...){
		  fdl <- featureData(object)
		  pos <- unlist(position(object))
		  snp <- unlist(lapply(fdl, isSnp))
		  chr <- unlist(lapply(fdl, chromosome))
		  df <- data.frame(position=pos, isSnp=snp, chromosome=chr)
		  rownames(df) <- unlist(featureNames(object))
		  fd <- as(df, "AnnotatedDataFrame")
		  fd2 <- as(fd, "GenomeAnnotatedDataFrame")
		  makeFeatureGRanges(fd2, genomeBuild(object))
	  })

setMethod("elementLengths", signature(x="gSetList"),
	  function(x){
		  adl <- assayDataList(x)
		  nm <- ls(adl)[[1]]
		  sapply(assayDataList(x)[[nm]], nrow)
	  })

setMethod("ncol", signature(x="gSetList"),
	  function(x){
		  adl <- assayDataList(x)
		  nm <- ls(adl)[[1]]
		  ncol(assayDataList(x)[[nm]][[1]])
	  })