Add files via upload

ConstructSpectra.R

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+#Read MGF 
+Construct_SpectraDF <- function(MGF_path)
+{
+  MGF <- readLines(MGF_path)
+
+  BEGINIONS <- "BEGIN IONS"
+  ENDIONS <- "END IONS"
+
+  Begin.index <- which(MGF %in% BEGINIONS) 
+  END.index <- which(MGF %in% ENDIONS)
+
+  NumberofSpectra <- length(Begin.index)
+  message(paste("Number of spectra identified in file", NumberofSpectra))
+
+  IndvidualSpectraDF <- c()
+  for (i in 1:NumberofSpectra)
+  {
+    Spectra <- MGF[Begin.index[i]:END.index[i]]
+    #Get locus of spectra 
+    SpectraID <- gsub(".*=(.+) .*", "\\1", Spectra[2])
+    IndvidualSpectraDF[i] <- paste(Spectra, collapse = "#") #replace # with \n when writing the file 
+    names(IndvidualSpectraDF)[i] <- SpectraID
+  }
+  IndvidualSpectraDF <- data.frame(IndvidualSpectraDF)
+
+  return(IndvidualSpectraDF)
+}

Installtion.R

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+if (!requireNamespace("BiocManager", quietly = TRUE))
+  install.packages("BiocManager")
+
+#Install rTandem 
+BiocManager::install("rTANDEM")
+library(rTANDEM)
+#Install shinyTandem 
+BiocManager::install("shinyTANDEM")
+library(shinyTANDEM)

Main.R

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+library(rTANDEM)
+source("ConstructSpectra.R")
+source("TandemSearch.R")
+source("RemoveIdentification.R")
+
+MGF.map <- Construct_SpectraDF(MGFPATH)
+#Apply tandem search
+Results <- TandemSearch()
+#Remove identified spectra
+Filtered.MGF <- RemoveIdentification(MGF.map, Results)

RemoveIdentification.R

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+RemoveIdentification <- function(SpectraDF, Search_results)
+{
+  IdentifiedSpectra <- Search_results@spectra
+  rownames(IdentifiedSpectra) <- IdentifiedSpectra$id 
+  #Remove identified spectra from MGF 
+  SpectraDF <- SpectraDF[-rownames(IdentifiedSpectra),]
+  return(SpectraDF)
+}
+

TandemSearch.R

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+TandemSearch <- function(taxon = 'yeast', format = 'peptide',
+                         FastaPath = system.file("extdata/fasta/scd.fasta.pro", package="rTANDEM"),
+                         MGFPath = system.file("extdata/200217-2-9-.mgf", package="rTANDEM"),
+                         InputPara = system.file("extdata/default_input.xml", package="rTANDEM"),
+                         Output_Path = paste(getwd(), "output.xml", sep="/"))
+{
+  taxonomy <- rTTaxo(taxon = taxon, format = format, URL = FastaPath)
+
+  param <- rTParam()
+  param <- setParamValue(param, 'protein', 'taxon', value="yeast")
+  param <- setParamValue(param, 'list path', 'taxonomy information', taxonomy)
+  param <- setParamValue(param, 'list path', 'default parameters',
+                         value=InputPara)
+  param <- setParamValue(param, 'spectrum', 'path',
+                         value=MGFPath)
+  param <- setParamValue(param, 'output', 'xsl path',
+                         value=system.file("extdata/tandem-input-style.xsl", package="rTANDEM"))
+  param <- setParamValue(param, 'output', 'path',
+                         value=Output_Path)
+
+  result.path <- tandem(param)
+
+  result.R <- GetResultsFromXML(result.path)
+  return(result.R)
+}