Merge pull request #16 from PNNL-Comp-Mass-Spec/feature/run-plexedpiper

Add run_plexedpiper function

NAMESPACE

@@ -23,6 +23,7 @@ export(remap_accessions_refseq_to_gene)
 export(remap_accessions_refseq_to_gene_fasta)
 export(remap_accessions_uniprot_to_gene)
 export(remap_accessions_uniprot_to_gene_fasta)
+export(run_plexedpiper)
 importFrom(Biostrings,readAAStringSet)
 importFrom(Biostrings,width)
 importFrom(IRanges,IRanges)
@@ -32,8 +33,13 @@ importFrom(MSnID,MSnID)
 importFrom(MSnID,MSnIDFilter)
 importFrom(MSnID,apply_filter)
 importFrom(MSnID,assess_missed_cleavages)
+importFrom(MSnID,compute_accession_coverage)
 importFrom(MSnID,convert_msgf_output_to_msnid)
+importFrom(MSnID,correct_peak_selection)
+importFrom(MSnID,extract_sequence_window)
 importFrom(MSnID,fetch_conversion_table)
+importFrom(MSnID,infer_parsimonious_accessions)
+importFrom(MSnID,map_mod_sites)
 importFrom(MSnID,mass_measurement_error)
 importFrom(MSnID,optimize_filter)
 importFrom(MSnID,psms)
@@ -79,6 +85,8 @@ importFrom(tibble,rownames_to_column)
 importFrom(tidyr,gather)
 importFrom(tidyr,spread)
 importFrom(utils,read.delim)
+importFrom(utils,read.table)
+importFrom(utils,write.table)
 importMethodsFrom(MSnID,"$<-")
 importMethodsFrom(MSnID,"psms<-")
 importMethodsFrom(MSnID,accessions)

R/run_plexedpiper.R

@@ -0,0 +1,248 @@
+#' @title Wrapper for PlexedPiper
+#'
+#' @description A wrapper function for PlexedPiper that performs all the steps
+#'   necessary to go from MS-GF+ and MASIC data to Reporter Ion Intensity (RII)
+#'   and Ratio Results tables used by the MoTrPAC Bioinformatics
+#'   Center (BIC).
+#'
+#' @param msgf_output_folder (character) Path to MSGF+ results folder
+#' @param fasta_file (character) Path and FASTA file name
+#' @param masic_output_folder (data.frame) MASIC results folder
+#' @param ascore_output_folder (data.frame) AScore results folder
+#' @param proteomics (character) Either "pr" - proteomics, "ph" -
+#'   phosphoproteomics, "ub" - ubiquitinomics, or "ac" - acetylomics
+#' @param study_design_folder (character) Folder containing the three study
+#'   design files: fractions.txt, samples.txt, and references.txt
+#' @param species (character) Scientific name of species (e.g. `Rattus
+#'   norvegicus`, `Homo sapiens`, etc.)
+#' @param annotation (character) Source for annotations: either `RefSeq` or
+#'   `Uniprot`
+#' @param global_results (character) Only for PTM experiments. Ratio results
+#'   from a global protein abundance experiment. If provided, it will infer
+#'   parsimonious set of accessions.
+#' @param write_results_to_file (logical) Whether to write the results to files.
+#' @param output_folder (character) Output folder name to save results. If not
+#'   provided, it will save it to the current directory.
+#' @param file_prefix (character) Prefix for the file name outputs
+#' @param save_env (logical) Whether to save the R environment to the output
+#'   folder.
+#' @param return_results (logical) Whether to return both ratio and rii results.
+#' @param verbose (logical) Whether to show messages describing steps.
+#'
+#' @return (list) If `return_results` is `TRUE`, it returns list with ratio and
+#'   RII data frames.
+#'
+#' @importFrom Biostrings readAAStringSet
+#' @importFrom utils read.table write.table
+#' @importFrom MSnID compute_accession_coverage correct_peak_selection
+#'   extract_sequence_window infer_parsimonious_accessions map_mod_sites
+#'
+#' @examples \dontrun{
+#' results <- run_plexedpiper(msgf_output_folder = "~/path/to/msgfplus/,
+#'                            fasta_file  = "~/path/to/fasta/sequence.fasta,
+#'                            masic_output_folder = "~/path/to/masic-results/",
+#'                            ascore_output_folder = "~/path/to/ascore-results/",
+#'                            proteomics = "ph",
+#'                            study_design_folder = "~/path/to/study-design/",
+#'                            species = "Rattus norvegicus",
+#'                            annotation = "RefSeq",
+#'                            global_results = "~/path/to/global/ratio.txt",
+#'                            output_folder = "~/path/to/pp-results/",
+#'                            file_prefix = "msgfplus-pp-results",
+#'                            return_results = TRUE,
+#'                            verbose = TRUE)
+#' }
+#' @export
+
+
+run_plexedpiper <- function(msgf_output_folder,
+                            fasta_file,
+                            masic_output_folder,
+                            ascore_output_folder = NULL,
+                            proteomics,
+                            study_design_folder,
+                            species,
+                            annotation,
+                            file_prefix = NULL,
+                            global_results = NULL,
+                            write_results_to_file = TRUE,
+                            output_folder = NULL,
+                            save_env = FALSE,
+                            return_results = FALSE,
+                            verbose = TRUE) {
+
+  if( is.null(write_results_to_file) & is.null(return_results) ){
+    stop("\nProvide either <write_results_to_file = TRUE> or <return_results = TRUE> or both. Both cannot be FALSE.")
+  }
+
+  if (verbose) {
+    message("Running PlexedPiper (the MSGF+ pipeline wrapper), with the following parameters:")
+    message("- Proteomics experiment:\"", proteomics, "\"")
+    message("- Species: \"", species, "\"")
+    message("- Annotation: \"", annotation, "\"")
+  }
+
+  if(is.null(file_prefix)){
+    file_prefix <- paste0("MSGFPLUS_", toupper(proteomics))
+    if(!is.null(global_results)){
+      file_prefix <- paste0(file_prefix,"-ip")
+    }
+  }
+
+  # Data loading
+  message("- Fetch study design tables")
+
+  study_design <- read_study_design(study_design_folder)
+  msnid <- read_msgf_data(msgf_output_folder)
+  if(!is.null(ascore_output_folder)) ascore <- read_AScore_results(ascore_output_folder)
+  masic_data <- read_masic_data(masic_output_folder,
+                                interference_score = TRUE)
+
+  fst <- Biostrings::readAAStringSet(fasta_file)
+  names(fst) <- sub("^(\\S*)\\s.*", "\\1", names(fst))
+
+  if (verbose) message("- Filtering MS-GF+ results.")
+  if (proteomics == "pr") {
+    if (verbose) message("   + Correct for isotope selection error")
+    msnid <- correct_peak_selection(msnid)
+  }
+
+  if (proteomics != "pr") {
+    if (verbose) message("   + Select best PTM location by AScore")
+    msnid <- best_PTM_location_by_ascore(msnid, ascore)
+
+    if (verbose) message("   + Apply PTM filter")
+    if (proteomics == "ph") {
+      reg.expr <- "grepl(\"\\\\*\", peptide)"
+    } else if (proteomics == "ac") {
+      reg.expr <- "grepl(\"#\", peptide)"
+    } else if (proteomics == "ub") {
+      psms(msnid) <- psms(msnid) %>% mutate(peptide = gsub("@", "#", peptide))
+      reg.expr <- "grepl(\"#\", peptide)"
+    }
+    msnid <- apply_filter(msnid, reg.expr)
+  }
+
+  if(verbose) message("   + Peptide-level FDR filter")
+  msnid <- filter_msgf_data(msnid, level = "peptide", fdr.max = 0.01)
+
+  if (proteomics == "pr") {
+    if (verbose) message("   + Protein-level FDR filter")
+    msnid <- compute_num_peptides_per_1000aa(msnid, path_to_FASTA = fasta_file)
+
+    msnid <- filter_msgf_data(msnid, level = "accession", fdr.max = 0.01)
+  }
+
+  if(verbose) message("   + Remove decoy sequences")
+  msnid <- apply_filter(msnid, "!isDecoy")
+
+  if (verbose) message("   + Concatenating redundant RefSeq matches")
+  msnid <- assess_redundant_protein_matches(msnid, collapse = ",")
+
+  if (verbose) message("   + Assessing non-inferable proteins")
+  msnid <- assess_noninferable_proteins(msnid, collapse = ",")
+
+  if(verbose) message("   + Inference of parsimonius set")
+  if (proteomics == "pr") {
+    prior <- character(0)
+  } else if (is.null(global_results)) {
+    if(verbose) message("     > Reference global proteomics dataset NOT provided")
+    prior <- character(0)
+  } else {
+    global_ratios <- read.table(global_results, header=TRUE, sep="\t")
+    prior <- unique(global_ratios$protein_id)
+  }
+
+  msnid <- infer_parsimonious_accessions(msnid, prior = prior)
+
+  if (proteomics == "pr") {
+    if (verbose) message("   + Compute protein coverage")
+    msnid <- compute_accession_coverage(msnid, fst)
+  }
+
+  if (proteomics != "pr") {
+    if(verbose) message("   + Mapping sites to protein sequence")
+    if (proteomics == "ph") {
+      mod_char = "*"
+    } else if (proteomics %in% c("ac", "ub")) {
+      mod_char = "#"
+    } else {
+      stop("Proteomics variable not supported.")
+    }
+
+    msnid <- map_mod_sites(msnid,
+                           fasta           = fst,
+                           accession_col   = "accession",
+                           peptide_mod_col = "peptide",
+                           mod_char        = mod_char,
+                           site_delimiter  = "lower")
+
+    if(verbose) message("   + Map flanking sequences")
+    msnid <- extract_sequence_window(msnid, fasta = fst)
+  }
+
+  if (verbose) message("- Filtering MASIC results.")
+  masic_data <- filter_masic_data(masic_data, 0.5, 0)
+
+  args <- list(msnid      = msnid,
+               masic_data = masic_data,
+               fractions  = study_design$fractions,
+               samples    = study_design$samples,
+               references = study_design$references,
+               annotation = annotation,
+               org_name   = species)
+
+  if (verbose) message("- Making results tables.")
+  if (proteomics == "pr") {
+    suppressMessages(rii_peptide <- do.call(make_rii_peptide_gl, args))
+    suppressMessages(results_ratio <- do.call(make_results_ratio_gl, args))
+  } else {
+    suppressMessages(rii_peptide   <- do.call(make_rii_peptide_ph,   args))
+    suppressMessages(results_ratio <- do.call(make_results_ratio_ph, args))
+  }
+
+  if (verbose) message("- Saving results.")
+
+  if(is.null(output_folder)){
+    output_folder <- getwd()
+  }
+
+  if(write_results_to_file){
+    if (!is.null(output_folder)) {
+      if (!dir.exists(file.path(output_folder))) {
+        dir.create(file.path(output_folder), recursive = TRUE)
+      }
+
+      filename = paste0(file_prefix, "-results_RII-peptide.txt")
+      write.table(rii_peptide,
+                  file      = file.path(output_folder, filename),
+                  sep       = "\t",
+                  row.names = FALSE,
+                  quote     = FALSE)
+      if(verbose) message("- RII file save to ",
+                          file.path(output_folder, filename))
+
+      filename = paste0(file_prefix, "-results_ratio.txt")
+      write.table(results_ratio,
+                  file      = file.path(output_folder, filename),
+                  sep       = "\t",
+                  row.names = FALSE,
+                  quote     = FALSE)
+      if(verbose) message("- RATIO file save to ",
+                          file.path(output_folder, filename))
+    }
+  }
+  if (save_env) {
+    fileenv = paste0(file_prefix, "-env.RData")
+    save.image(file = file.path(output_folder, fileenv))
+    if(verbose) message("- R environment saved to ",
+                        file.path(output_folder, fileenv))
+  }
+
+  if (verbose) message("Done!")
+
+  if(return_results){
+    return(list(rii_peptide = rii_peptide, results_ratio = results_ratio))
+  }
+}
+