R/read_msgf_data.R

In vladpetyuk/PlexedPiper: Pipeline for isobaric quantification.

#' Reading MSGF Results. Generic.
#'
#' Reading MSGF output from a single directory
#'
#' @param path_to_MSGF_results (path string) to directory with MSGF results for all datasets
#' @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
read_msgf_data <- function(path_to_MSGF_results, suffix = NULL){
   
   if (is.null(suffix)) {
      for (pattern in c("_msgfplus_syn.txt", "_msgfdb_syn.txt", "_syn.txt")) {
         if (length(list.files(path_to_MSGF_results, pattern)) > 0) {
            suffix <- pattern
            break
         }
      }
   }
   
   if (is.null(suffix) | (length(list.files(path_to_MSGF_results, suffix)) == 0)) {
      stop("MS-GF+ results not found.")
   }
   
   x <- collate_files(path_to_MSGF_results, suffix)
   msnid <- convert_msgf_output_to_msnid(x)
   return(msnid)
}


# helper function
convert_msgf_output_to_msnid <- function(x){
   suppressMessages(msnid <- MSnID("."))
   x <- x %>% mutate(accession = Protein,
             calculatedMassToCharge = (MH + (Charge-1)*MSnID:::.PROTON_MASS)/Charge,
             chargeState = Charge,
             experimentalMassToCharge = PrecursorMZ,
             isDecoy = grepl("^XXX", Protein),
             spectrumFile = Dataset,
             spectrumID = Scan) %>%
      rename(peptide = Peptide)
   # clean peptide sequences
   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)
#' }