#' 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
}
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