R/utils.R

In LieberInstitute/qsvaR: Generate Quality Surrogate Variable Analysis for Degradation Correction

#' Remove version number from Gencode/Ensembl transcript names
#'
#' This function removes the Gencode/ENSEMBL version from the transcript ID, while protecting _PAR_Y suffixes if present
#'
#' @param txnames A `character()` vector of GENCODE or ENSEMBL transcript IDs
#'
#'
#' @return A
#'  `character()` vector of transcript names without versioning
#'
#' @export
#'
#' @examples
#' ensIDs <- normalize_tx_names(rownames(rse_tx))
normalize_tx_names <- function(txnames) {
    sub("(ENST\\d+)\\.\\d+(.*)$", "\\1\\2", txnames, perl = TRUE)
}


#' Check validity of transcript vectors and return a vector matching indexes in tx1
#'
#' This function is used to check if tx1 and tx2 are GENCODE or ENSEMBL transcript IDs
#' and return an integer vector of tx1 transcript indexes that are in tx2.
#'
#' @param txnames A `character()` vector of GENCODE or ENSEMBL transcript IDs.
#' @param sig_tx A `character()` vector of GENCODE or ENSEMBL signature transcript IDs.
#'
#'
#' @return A
#'  `integer()` vector of `txnames` transcript indexes in `sig_tx`.
#'
#' @export
#'
#' @examples
#' sig_tx <- select_transcripts(cell_component = TRUE)
#' whichTx <- which_tx_names(rownames(rse_tx), sig_tx)
which_tx_names <- function(txnames, sig_tx) {
    ## Between releases 25 and 43, PAR genes and transcripts had the "_PAR_Y" suffix appended to their identifiers.
    ## Since release 44, these have their own IDs
    if (!all(grepl("^ENST\\d+", txnames))) {
        stop("The transcript names must be ENSEMBL or Gencode IDs (ENST...)")
    }
    if (!all(grepl("^ENST\\d+", sig_tx))) {
        stop("The signature transcript names must be ENSEMBL or Gencode IDs (ENST...)")
    }
    ## normalize the transcript names
    r_tx <- normalize_tx_names(txnames)
    s_tx <- normalize_tx_names(sig_tx)
    which(r_tx %in% s_tx)
}