Issue 109 a:

R/accnum.R

@@ -0,0 +1,144 @@
+
+
+#' Convert UniProt IDs to NCBI RefSeq Accessions
+#'
+#' This function takes one or more UniProt IDs and returns the corresponding NCBI RefSeq accessions.
+#' It uses the org.Hs.eg.db package to perform the mapping.
+#'
+#' @param uniprot_ids A character vector of UniProt IDs.
+#' @return A data frame with columns 'UNIPROT' and 'REFSEQ', mapping UniProt IDs to RefSeq accessions.
+#'         Returns an empty data frame if no mappings are found.
+#' @examples
+#' \dontrun{
+#'   uniprot_ids <- c("P04217", "P01023")
+#'   refseq_accessions <- up2ncbi(uniprot_ids)
+#'   print(refseq_accessions)
+#' }
+#' @importFrom AnnotationDbi select
+#' @import org.Hs.eg.db
+#' @export
+up2ncbi <- function(uniprot_ids) {
+  # Check if input is provided
+  if (length(uniprot_ids) == 0) {
+    stop("No UniProt IDs provided.")
+  }
+
+  # Perform the mapping
+  tryCatch({
+    mapping <- AnnotationDbi::select(
+      org.Hs.eg.db,
+      keys = uniprot_ids,
+      columns = "REFSEQ",
+      keytype = "UNIPROT"
+    )
+
+    # Check if any mappings were found
+    if (nrow(mapping) == 0) {
+      warning("No NCBI accessions found for the given UniProt IDs.")
+    }
+
+    return(mapping)
+  }, error = function(e) {
+    stop(paste("Error in mapping:", e$message))
+  })
+}
+
+
+
+#' Convert NCBI RefSeq Accessions to UniProt IDs
+#'
+#' This function takes one or more NCBI RefSeq accession numbers and returns the corresponding UniProt IDs.
+#' It uses the org.Hs.eg.db package to perform the mapping.
+#'
+#' @param ncbi_accessions A character vector of NCBI RefSeq accession numbers.
+#' @return A data frame with columns 'REFSEQ' and 'UNIPROT', mapping RefSeq accessions to UniProt IDs.
+#'         Returns NA for UniProt if no mapping is found.
+#' @examples
+#' \dontrun{
+#'   ncbi_accessions <- c("NP_000005.2", "NP_000007.1")
+#'   uniprot_ids <- ncbi2up(ncbi_accessions)
+#'   print(uniprot_ids)
+#' }
+#' @importFrom AnnotationDbi select
+#' @import org.Hs.eg.db
+#' @export
+ncbi2up <- function(ncbi_accessions) {
+  # Check if input is provided
+  if (length(ncbi_accessions) == 0) {
+    stop("No NCBI accessions provided.")
+  }
+
+  # Strip version numbers from accessions
+  stripped_accessions <- gsub("\\.[0-9]+$", "", ncbi_accessions)
+
+  # Perform the mapping
+  tryCatch({
+    mapping <- AnnotationDbi::select(
+      org.Hs.eg.db,
+      keys = stripped_accessions,
+      columns = "UNIPROT",
+      keytype = "REFSEQ"
+    )
+
+    # Check if any mappings were found
+    if (nrow(mapping) == 0) {
+      warning("No UniProt IDs found for the given NCBI accessions.")
+    }
+
+    return(mapping)
+  }, error = function(e) {
+    stop(paste("Error in mapping:", e$message))
+  })
+}
+
+
+
+#' Convert NCBI Protein Accessions to IPG (Identical Protein Group) IDs
+#'
+#' This function takes one or more NCBI protein accession numbers and returns the corresponding
+#' IPG (Identical Protein Group) IDs. It uses the NCBI E-utilities API via the rentrez package
+#' to perform the mapping.
+#'
+#' @param ncbi_ids A character vector of NCBI protein accession numbers.
+#' @return A data frame with columns 'NCBI' and 'IPG', mapping NCBI protein accessions to IPG IDs.
+#'         Returns an empty data frame if no mappings are found.
+#' @examples
+#' \dontrun{
+#'   ncbi_ids <- c("NP_000005.2", "NP_000007.1")
+#'   ipg_mappings <- ncbi2ipg(ncbi_ids)
+#'   print(ipg_mappings)
+#' }
+#' @importFrom rentrez entrez_search
+#' @export
+ncbi2ipg <- function(ncbi_ids) {
+  # Check if input is provided
+  if (length(ncbi_ids) == 0) {
+    stop("No NCBI IDs provided.")
+  }
+
+  # Perform the mapping
+  tryCatch({
+    # Search the IPG database for each NCBI ID
+    results <- lapply(ncbi_ids, function(id) {
+      search <- entrez_search(db = "ipg", term = paste0(id, "[PACC]"))
+      if (search$count > 0) {
+        data.frame(NCBI = id, IPG = search$ids, stringsAsFactors = FALSE)
+      } else {
+        NULL
+      }
+    })
+
+    # Combine results into a single data frame
+    mapping <- do.call(rbind, results)
+
+    # Check if any mappings were found
+    if (is.null(mapping) || nrow(mapping) == 0) {
+      warning("No IPG mappings found for the given NCBI IDs.")
+      mapping <- data.frame(NCBI = character(0), IPG = character(0), stringsAsFactors = FALSE)
+    }
+
+    return(mapping)
+  }, error = function(e) {
+    stop(paste("Error in mapping:", e$message))
+  })
+}