R/filter.R

In mbootwalla/MethylHose: Automated down stream processing of methylation data

applyFilters <- function(x, filter="all", custom.filter)
{
	if(missing(x) || !is(x, "matrix")) stop("Please provide a valid matrix as input \n")
	if(!any(grepl("^cg", rownames(x)))) stop("Probe names for the beta values matrix are not standard Illumina 450k probe names \n")
	
	if(!(all(filter %in% c("none", "noncg", "sex", "snp", "rpt", "all", "custom")))) stop("Please provide a valid filter. See '?applyFilters' for valid filters \n")
	
	if("none" %in% filter){
		message("Not performing any filtering as Filter : none was specified \n\n") 
		return(x)
	}
	
	if("all" %in% filter){
		data(filters)
		if(length(filter) > 1) warning("Multiple filter types specified along with type 'all'. Overriding the other filters and applying only the 'all' filter \n")
		message("Applying Filter : all \n\n")
		filter.all <- filters$filter.all
		x <- x[-which(rownames(x) %in% filter.all), , drop=FALSE]
		return(x)
	}

	if("custom" %in% filter){
		if(missing(custom.filter)) stop("Please provide a custom filter\n")
		if(!is(custom.filter, "character")) stop("Custom filter should be a chracter vector containing probe names that are to be filtered out \n")
		if(!any(grepl("^cg", custom.filter)) && !any(grepl("^rs", custom.filter)) && !any(grepl("^ch", custom.filter))) {
			stop("Custom filter contains non-standard Illumina 450k probe names \n")
		}
		message("Applying provided custom filter \n\n")
		x <- x[-which(rownames(x) %in% custom.filter), , drop=FALSE]
		return(x)
	}

	if(!("none" %in% filter) && !("all" %in% filter) && !("custom" %in% filter)){
		data(filters)
		f <- paste("filter", filter, sep=".")
		message(paste("Applying filters : ", paste(filter, collapse = ", "), "\n\n", sep=""))
		filter.apply <- unique(unlist(lapply(f, function(x){filters[f]})))
		x <- x[-which(rownames(x) %in% filter.apply), , drop=FALSE]
		return(x)
	}
}

percentMFilter <- function(x, percent = 10)
{
	if(!is(x, "SimpleList")){
		stop("Data should be a SimpleList object \n")
	}
	message(paste("Retaining probes methylated in", percent, "percent of Tumor samples\n", sep=" "))
	datT <- x$DICHOTOMIZED$Tumor.Dichotomized
	#datN <- x$DICHOTOMIZED$Normal.Dichotomized
	datT.percentM <- datT[which(((rowSums(datT)/ncol(datT))*100) > percent),]
	#keep.probes.T <- match(rownames(datT.percentM), rownames(datT))
	#keep.probes.N <- match(rownames(datT.percentM), rownames(datN))
	x$FILTERED <- SimpleList("Tumor.Filtered" = datT.percentM)
	return(x)
}