R/id_conversion_all.r

In GeoTcgaData: Processing various types of data on GEO and TCGA

## quiets concerns of R CMD check re: the .'s that appear in pipelines
# if(getRversion() >= "2.15.1") utils::globalVariables("hgnc_file")

#' Gene id conversion types
#'
#' @return a vector 
#' @export
#'
#' @examples
#' id_ava()
id_ava <- function() {
    return(colnames(hgnc_file))
}


#' Gene id conversion
#'
#' @param from one of `id_ava()`
#' @param to one of `id_ava()`
#' @param IDs the gene id which needed to convert
#' @param na.rm Whether to remove lines containing NA
#'
#' @return a vector of genes
#' @export
#'
#' @examples
#' id_conversion_vector("symbol", "Ensembl_ID", 
#'     c("A2ML1", "A2ML1-AS1", "A4GALT", "A12M1", "AAAS"))
id_conversion_vector <- function(from, to, IDs, na.rm = FALSE) {

    # Compatible with previous versions
    if(from == "RefSeq_ID") from <- "refseq_accession"
    if(from == "Ensembl_ID") from <- "ensembl_gene_id"
    if(from == "NCBI_Gene_ID") from <- "NCBI Gene ID"
    if(from == "UCSC_ID") from <- "ucsc_id"
    if(from == "UniProt_ID") from <- "uniprot_ids"
    
    if(to == "RefSeq_ID") to <- "refseq_accession"
    if(to == "Ensembl_ID") to <- "ensembl_gene_id"
    if(to == "NCBI_Gene_ID") to <- "NCBI Gene ID"
    if(to == "UCSC_ID") to <- "ucsc_id"
    if(to == "UniProt_ID") to <- "uniprot_ids"    

    from <- match.arg(from, id_ava())
    to <- match.arg(to, id_ava())    
    loc <- which(hgnc_file[, from] %in% IDs)
    if (length(loc) > 0) {
        results_mat <- data.frame(from = hgnc_file[loc, from], to = hgnc_file[loc, to])
        msg <- paste(format(100 * sum(!is.na(results_mat$to)) / 
                     length(IDs), digits=4), "%", 
                     " were successfully converted.", sep = "")
        message(msg)
        if (na.rm == TRUE) 
            results_mat <- results_mat[!is.na(results_mat$to), ]
    } else {
        stop("Failed to match")
    }
    return(results_mat)
}