Nothing
#' @title Get Entrez annotation
#' @description This function retrieves Entrez annotation data from NCBI.
#' @param entrezIds A vector of Entrez IDs.
#' @return A data frame with Entrez annotation or NULL if retrieval fails.
#' The columns are ID (Entrez ID), Symbol, Description, OtherDesignations, OtherAliases, and Chromosome.
#' @examples
#'
#' library(RCPA)
#' geneAnno <- getEntrezAnnotation(c("77267466", "77267467"))
#'
#' @importFrom httr POST content
#' @importFrom dplyr %>%
#' @export
getEntrezAnnotation <- function(entrezIds) {
# Check for required package and exit gracefully if missing
if (!requireNamespace("XML", quietly = TRUE)) {
warning("The XML package is not available. Please install it to use this function.")
return(NULL)
}
# Set URL and query parameters for NCBI Entrez
url <- "https://eutils.ncbi.nlm.nih.gov/entrez/eutils/esummary.fcgi"
query <- list(
db = "gene",
id = unique(as.character(entrezIds)) %>% paste0(collapse = ",")
)
# Attempt to retrieve data, with graceful failure if unsuccessful
xml <- tryCatch({
res <- POST(url, query = query) %>% content(as = "text")
XML::xmlParse(res)
}, error = function(e) {
warning("Data from NCBI could not be retrieved. Please check your internet connection or try again later.")
return(NULL)
})
# If XML retrieval failed, return NULL
if (is.null(xml)) {
return(NULL)
}
# Parse XML and extract data
xpath <- "//DocumentSummary"
results <- XML::xpathApply(xml, xpath, function(xmlDoc) {
listDat <- XML::xmlToList(xmlDoc)
data.frame(
ID = listDat$.attrs[["uid"]],
Symbol = ifelse(is.null(listDat$Name), NA, listDat$Name),
Description = ifelse(is.null(listDat$Description), NA, listDat$Description),
OtherDesignations = ifelse(is.null(listDat$OtherDesignations), NA, listDat$OtherDesignations),
OtherAliases = ifelse(is.null(listDat$OtherAliases), NA, listDat$OtherAliases),
Chromosome = ifelse(is.null(listDat$Chromosome), NA, listDat$Chromosome),
stringsAsFactors = FALSE
)
}) %>%
do.call(what = rbind) %>%
`rownames<-`(.$ID)
return(results)
}
Any scripts or data that you put into this service are public.
Add the following code to your website.
For more information on customizing the embed code, read Embedding Snippets.