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#' Transform id among symbol, entrezid, ensembl and uniprot.
#' @param id Gene ids or protein ids.
#' @param transTo Transform to what type. User could select one or more from
#' "symbol", "entrez", "ensembl" or "uniprot."
#' @param org Latin organism shortname from `ensOrg_name`. Default is human.
#' @param unique Logical, if one-to-many mapping occurs, only keep one record with fewest NA. Default is FALSE.
#' @param keepNA If some id has no match at all, keep it or not. Default is FALSE.
#' @param hgVersion Select human genome build version from "v38" (default) and "v19".
#' @importFrom dplyr filter pull select distinct arrange all_of filter_at vars any_vars
#' @importFrom rlang .data
#'
#' @return data frame, first column is input id and others are converted id.
#' @export
#'
#' @examples
#' \donttest{
#' # example1:
#' transId(
#' id = c("Cyp2c23", "Fhit", "Gal3st2b", "Trp53", "Tp53"),
#' transTo = "ensembl", org = "mouse", keepNA = FALSE
#' )
#'
#' ## example2: input id with one-to-many mapping and fake one
#' transId(
#' id = c("MMD2", "HBD", "RNR1", "TEC", "BCC7", "FAKEID", "TP53"),
#' transTo = c("entrez", "ensembl"), keepNA = TRUE
#' )
#'
#' # example3: auto-recognize ensembl version number
#' transId("ENSG00000141510.11", "symbol")
#'
#' # example4: search genes with case-insensitive
#' transId(c('nc886','ezh2','TP53'),transTo = "ensembl",org = 'hs',unique = TRUE)
#' }
#'
transId <- function(id,
transTo,
org = "hs",
unique = FALSE,
keepNA = FALSE,
hgVersion = c("v38","v19")) {
#--- args ---#
org <- mapEnsOrg(organism = tolower(org))
hgVersion <- match.arg(hgVersion)
# if id has ensembl version, remove them
# if(all(all %>% stringr::str_detect(.,'ENS'))) id <- stringr::str_split(id, "\\.", simplify = T)[, 1]
transTo <- sapply(tolower(transTo), function(x) {
if (grepl(x, "entrezid")) x <- "entrezid"
if (grepl(x, "ensemblid")) x <- "ensembl"
if (grepl(x, "symbolid")) x <- "symbol"
if (grepl(x, "uniprot")) x <- "uniprot"
return(x)
}) %>% as.character()
if (!all(tolower(transTo) %in% c("symbol", "entrezid", "ensembl", "uniprot"))) {
stop("\nChoose 'transTo' argument from: \nsymbol | entrezid | ensembl | uniprot")
}
#--- codes ---#
tryCatch(
{
all <- ensAnno(org,hgVersion = hgVersion)
if(all(id %>% stringr::str_detect(.,'ENS'))) id <- stringr::str_split(id, "\\.", simplify = T)[, 1]
id <- replace_greek(id)
keytype <- gentype(id = id, data = all, org = org) %>% tolower()
if(keytype != 'symbol'){
res <- genInfo(id, org, unique, keepNA,hgVersion) %>%
dplyr::mutate( !! keytype := input_id) %>%
dplyr::select(input_id, all_of(transTo)) %>%
distinct()
}else{
res <- genInfo(id, org, unique, keepNA,hgVersion) %>%
dplyr::select(input_id, all_of(transTo)) %>%
distinct()
}
},
error = function(e) {
message('Maybe your "trans_to" argument is wrong, please check again...')
}
)
if (!keepNA) {
res <- res %>%
filter_at(vars(!input_id), any_vars(!is.na(.)))
}
# replace back greek letter
res$input_id = replace_back(res$input_id)
# convert factor to character
res[] <- lapply(res, as.character)
## calculate percent
n_new <- sapply(transTo, function(x) {
# x = transTo[1]
res %>%
dplyr::select(input_id, all_of(x)) %>%
stats::na.omit() %>%
distinct(input_id) %>%
nrow()
})
percent <- paste(round(100 * n_new / length(unique(id)), 2), "%", sep = "")
sapply(seq_along(transTo), function(x) {
# x = 1
message(percent[x], " genes are mapped to ", transTo[x])
}) %>% invisible()
return(res)
}
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