R/fastMap.R

Defines functions fastMap

Documented in fastMap

# fastMap.R

#' Map an ID to its associated HGNC gene symbol.
#'
#' \code{fastMap} accesses the associated hash table
#' (\code{fastMapUniProt} for UniProt IDs or
#' \code{fastMapUniENSP} for Ensembl protein IDs) and returns the
#' associated HGNC gene symbol. Unmapped IDs will be returned as is and
#' will be stored in an global option \code{rete.unmapped}.
#'
#' @param ID a vector of IDs to be mapped.
#' @param hashTable the hash table to perform lookups on.
#' @param type the type of the unmapped ID.
#' @param quietly logical. If FALSE, a warning is generated if IDs
#'                could not be mapped.
#' @param dev logical. For development only. If TRUE, all checks are made
#'            but instead of actually mapping, the original IDs are returned.
#' @return the mapped HGNC symbol or \code{ID} if not found.
#'
#' @family fastMap functions
#'
#' @examples
#' \dontrun{
#' fastMap("ENSG00000121410", fastMapENSP, type = "ENSP")
#' fastMap(c("Q9NQ94", "P01023"), fastMapUniProt)
#' }
#' @export
fastMap <- function(ID,
                    hashTable,
                    type = "UniProt",
                    quietly = FALSE,
                    dev = FALSE) {
# ToDo: remove dev option once development is done

    if (!is.null(attributes(hashTable)$type)) {
        if (type != attributes(hashTable)$type) {
            errorMessage <- sprintf("Expected hash table type: %s. Supplied hash table type: %s",
                                    type, attributes(hashTable)$type)
            stop(errorMessage)
        }
    } else {
        errorMessage <- "Supplied hash table does not have a type attribute."
        stop(errorMessage)
    }
    IDLength = length(ID)
    out <- character(length = IDLength)
    for (i in 1:IDLength) {
        if (dev) {   # ToDo remove this option when development is done.
            out[i] <- ID[i]
        } else {
            lookUp <- hashTable[[ID[i]]]
            if (is.null(lookUp)) {
                out[i] <- NA
            } else {
                out[i] <- lookUp
            }
        }
    }

    # Address unmapped IDs
    unmappedCount <- sum(is.na(out))
    if (unmappedCount) {
        iNA <- which(is.na(out))
        out[iNA] <- ID[iNA]
        # Export unmapped IDs to the global option rete.unmapped
        options(rete.unmapped = ID[iNA])
        warningMessage <- sprintf("%d of %d IDs could not be mapped, %s %s",
                                  unmappedCount,
                                  IDLength,
                                  "see getOptions('rete.unmapped')",
                                  "to list them all.")
        if (!quietly) {
            warning(warningMessage)
        }
    }
    return(out)
}

# [END]
hyginn/ekplektoR documentation built on May 17, 2017, 12:08 a.m.