R/z_dms_read_msgf_data.R

In vladpetyuk/PlexedPiper: Pipeline for isobaric quantification.

#' #' Reading MSGF Results. Generic.
#' #'
#' #' Reading MSGF output from PNNL's DMS
#' #'
#' #' @param DataPkgNumber (Numeric or Character vector) containing Data Package ID(s) located in DMS
#' #' @return (MSnID) MSnID object
#' #' @importFrom dplyr mutate
#' #' @importFrom MSnID MSnID
#' #' @importMethodsFrom MSnID psms<-
#' #' @examples
#' #' path_to_MSGF_results <- system.file("extdata/global/msgf_output", package = "PlexedPiperTestData")
#' #' msnid <- read_msgf_data(path_to_MSGF_results)
#' #' print(msnid)
#' #' head(MSnID::psms(msnid))
#'
#' #' @export
#' dms_read_msms_data <- function(DataPkgNumber){
#'   msnid <- MSnID(".")
#'   # accession -> Protein
#'   # calculatedMassToCharge -> f(MH, Charge) MSnID:::.PROTON_MASS
#'   # (MH + (Charge-1)*MSnID:::.PROTON_MASS)/Charge
#'   # chargeState -> Charge
#'   # experimentalMassToCharge -> PrecursorMZ
#'   # isDecoy -> grep("^XXX", Protein)
#'   # peptide -> Peptide
#'   # spectrumFile -> Dataset
#'   # spectrumID -> Scan
#'
#'   if (!is.null(DataPkgNumber)) {
#'
#'     # Fetch job records for data package(s)
#'     if (length(DataPkgNumber) > 1) {
#'       job_rec_ls <- lapply(DataPkgNumber, get_job_records_by_dataset_package)
#'       jobRecords <- Reduce(rbind, job_rec_ls)
#'     }
#'
#'     else {
#'       jobRecords <- get_job_records_by_dataset_package(DataPkgNumber)
#'     }
#'
#'     jobRecords <- jobRecords[grepl("MSGFPlus", jobRecords$Tool),]
#'
#'     x <- get_results_for_multiple_jobs.dt(jobRecords)
#'     x <- x %>%
#'       mutate(accession = Protein,
#'              calculatedMassToCharge = (MH + (Charge-1)*MSnID:::.PROTON_MASS)/Charge,
#'              chargeState = Charge,
#'              experimentalMassToCharge = PrecursorMZ,
#'              isDecoy = grepl("^XXX", Protein),
#'              peptide = Peptide,
#'              spectrumFile = Dataset,
#'              spectrumID = Scan)
#'
#'     x <- mutate(x, pepSeq = MSnID:::.get_clean_peptide_sequence(peptide))
#'
#'     psms(msnid) <- x
#'     return(msnid)
#'   }
#'
#' }
#'
#'
#' #' # (yet) non-exported helper function
#' #' #' @importFrom Biostrings AA_STANDARD
#' #' #' @importFrom purrr map_chr
#' #' #' @importFrom stringr str_replace_all
#' #' peptide_to_sequence <- function(pep){
#' #'    pep_no_flank <- sub(".\\.(.*)\\..", "\\1", pep)
#' #'    present_chars <- paste0(pep_no_flank, collapse = '') %>%
#' #'       strsplit(split='') %>%
#' #'       `[[`(1) %>%
#' #'       unique()
#' #'    other_chars <- setdiff(present_chars, AA_STANDARD)
#' #'    if(length(other_chars) > 0){
#' #'       message("Detected extra chararacters in the peptide sequences!")
#' #'       # erase other chars in TrimmedPeptide
#' #'       other_chars_pttrn <- other_chars %>%
#' #'          map_chr(~paste0("\\",.x)) %>%
#' #'          paste0(collapse='') %>%
#' #'          paste0("[",.,"]")
#' #'       pep_clean <- str_replace_all(pep_no_flank, other_chars_pttrn, "")
#' #'    }
#' #'    return(pep_clean)
#' #' }