R/read_msgf_data_from_DMS.R

In vladpetyuk/PlexedPiper: Pipeline for isobaric quantification.

#' 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
#' msnid <- read_msgf_data_from_DMS(3442)
#' print(msnid)
#' head(MSnID::psms(msnid))

#' @export
read_msms_data_from_DMS <- function(DataPkgNumber) {
  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)
    msnid <- convert_msgf_output_to_msnid(x)
    return(msnid)
  }

}