R/retrieve.probesets.R

In microbiome/HITChipDB: HITChipDB

#' retrieve.probesets
#' 
#' List probes for each probeset
#'
#' @param tax.table data.frame with oligo - phylotype 
#' 	  		 mapping information
#' @param level phylotype level for probesets
#' @param name specify phylotypes to check (optional)
#'
#' @return A list. Probes for each phylotype.
#'
#' @export
#' @references See citation('microbiome') 
#' @author Contact: Leo Lahti \email{microbiome-admin@@googlegroups.com}
#' @keywords utilities
retrieve.probesets <- function(tax.table, level = "species", name = NULL) {

    tax.table <- as.data.frame(tax.table)

    # If name not given, pick all
    if (is.null(name)) {
        name <- unique(as.character(tax.table[[level]]))
    }
    
    phylo <- tax.table[tax.table[[level]] %in% name, ]
    
    if (is.factor(phylo[[level]])) {
        phylo[[level]] <- droplevels(phylo[[level]])
    }
    
    phylo.list <- split(phylo, phylo[[level]])
    probesets <- lapply(phylo.list, function(x) {
        as.character(unique(x$oligoID))
    })
    names(probesets) <- names(phylo.list)
    
    probesets
    
}