R/trimToTaxaLevel.R

In HMPTrees: Statistical Object Oriented Data Analysis of RDP-Based Taxonomic Trees from Human Microbiome Data

trimToTaxaLevel <-
function(data, level="genus", eliminateParentNodes=FALSE, trimBelow=NULL, split="."){
	if(missing(data))
		stop("A valid data set is required.")
	
	maxLevel <- getTaxaDepth(level)
	
	nameSplit <- strsplit(as.character(rownames(data)), split, fixed=TRUE)
	lowerLevels <- NULL
	for(l in 1:nrow(data)){ 
		if(length(nameSplit[[l]]) == maxLevel){
			lowerLevels <- c(lowerLevels, l)
			if(eliminateParentNodes && is.null(trimBelow))
				rownames(data)[l] <- nameSplit[[l]][maxLevel]
		}else if(!is.null(trimBelow) && is.logical(trimBelow)){
			if(length(nameSplit[[l]]) < maxLevel && trimBelow){
				lowerLevels <- c(lowerLevels, l)
			}else if(length(nameSplit[[l]]) > maxLevel && !trimBelow){
				lowerLevels <- c(lowerLevels, l)
			}
		}
	}
	
	data <- data[lowerLevels,, drop=FALSE]
	return(data)
}