add function

R/genGO.R

@@ -49,7 +49,8 @@ genGO <- function(id,
   stopifnot(is.character(id))
   if (missing(universe)) universe <- NULL
 
-  bioc_org <- mapBiocOrg(tolower(org))
+  bioc_org <- mapBiocOrg(org)
+  org <- mapEnsOrg(org)
   pkg <- paste0("org.", bioc_org, ".eg.db")
   keyType <- gentype(id, org)
 
@@ -72,7 +73,7 @@ genGO <- function(id,
   }
 
   if (use_symbol) {
-    info <- genInfo(id, org, unique = T) %>% na.omit()
+    info <- genInfo(id, org, unique = T)
     new_geneID <- stringr::str_split(ego$geneID, "\\/") %>%
       lapply(., function(x) {
         info %>%

R/genInfo.R

@@ -36,21 +36,22 @@ genInfo <- function(id,
   rm(list = paste0(org, "_anno"), envir = .GlobalEnv)
 
   tmp1 <- data.frame(input_id = id)
-  tmp2 <- all %>% dplyr::filter(eval(parse(text = keytype)) %in% id)
 
   if(any(c("symbol", "uniprot") %in% colnames(all))){
+    tmp2 <- all %>% dplyr::filter(eval(parse(text = keytype)) %in% id)
     tmp3 <- tmp2 %>%
       dplyr::select(-c("symbol", "uniprot")) %>%
-      apply(., 1, is.na)
+      apply(., 1, is.na) %>%
+      as.data.frame()
   }
 
   ## keep each id even has no info
   # only symbol id needs  to consider alias
   if (keytype != "symbol") {
     gene_info <- merge(tmp1, tmp2, by.x = "input_id", by.y = keytype, all.x = T)
   } else if (any(apply(tmp3, 2, sum) == nrow(tmp3))) {
-    # if only symbol and uniprot are not NA
-    tmp2 <- tmp2 %>% dplyr::filter_at(dplyr::vars(-symbol, -uniprot), dplyr::all_vars(!is.na(.)))
+    # only symbol and uniprot are not NA <= import gene from uniprot
+    tmp2 <- tmp2[-which(apply(tmp3, 2, sum) == nrow(tmp3)),]
     gene_info <- merge(tmp1, tmp2, by.x = "input_id", by.y = keytype, all.x = T) %>%
       dplyr::arrange(id) %>%
       dplyr::mutate(symbol = dplyr::case_when(input_id %in% tmp2$symbol ~ input_id)) %>%

R/genKEGG.R

@@ -46,12 +46,13 @@ genKEGG <- function(id,
   stopifnot(is.character(id))
   if (missing(universe)) universe <- NULL
 
-  kegg_org <- mapKeggOrg(tolower(org))
+  kegg_org <- mapKeggOrg(org)
+  org <- mapEnsOrg(org)
   keyType <- gentype(id, org)
 
   if (!keyType %in% c("ENTREZID")) {
     message(paste0(keyType), " gene will be mapped to entrez id")
-    trans_id <- suppressMessages(transId(id, "entrezid", kegg_org)) %>% stringi::stri_remove_na()
+    trans_id <- suppressMessages(transId(id, "entrezid", org)) %>% stringi::stri_remove_na()
   } else {
     trans_id <- id
   }
@@ -61,7 +62,7 @@ genKEGG <- function(id,
   #--- codes ---#
   keg <- suppressMessages(
     clusterProfiler::enrichKEGG(
-      gene = trans_id, organism = org, keyType = "kegg",
+      gene = trans_id, organism = kegg_org, keyType = "kegg",
       pvalueCutoff = pvalueCutoff,
       pAdjustMethod = pAdjustMethod,
       qvalueCutoff = qvalueCutoff,

R/transID.R

@@ -2,8 +2,8 @@
 #' @param id Gene ids.
 #' @param trans_to Transform to which type, one of "symbol", "entrezid",
 #'   "ensembl" and "uniprot."
-#' @param org Organism name from `biocOrg_name`, both full name and short name are fine.
-#' @param unique Logical to keep only one unique mapped ID, default is FALSE.
+#' @param org Short latin name from `ensOrg_name_data`.
+#' @param unique If keep only one unique mapped ID when one-to-many gene occurs, default is FALSE.
 #' @importFrom dplyr %>% filter pull select distinct arrange all_of
 #' @importFrom tibble add_row
 #' @importFrom stats na.omit