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## 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)
}
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