changeset 31:cb56479f7aca draft

Uploaded

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/pre_process_protein_name_set.R	Thu Jan 28 13:53:56 2016 -0500
@@ -0,0 +1,124 @@
+#######################################################################################
+# R-code: Protein Name and Tukey's Normalization
+# Author: Adam L Borne
+# Contributers: Paul A Stewart, Brent Kuenzi
+#######################################################################################
+# Assigns uniprot id from MaxQuant peptides file. Filters and normalizes the
+# intensities of each proteins. Resulting in a one to one list of intensities to 
+# uniprot id.
+#######################################################################################
+# Copyright (C)  Adam L Borne.
+# Permission is granted to copy, distribute and/or modify this document
+# under the terms of the GNU Free Documentation License, Version 1.3
+# or any later version published by the Free Software Foundation;
+# with no Invariant Sections, no Front-Cover Texts, and no Back-Cover Texts.
+# A copy of the license is included in the section entitled "GNU
+# Free Documentation License".
+#######################################################################################
+## REQUIRED INPUT ##
+
+# 1) peptides_file: MaxQuant peptides file. 
+#######################################################################################
+ins_check_run <- function() {
+  if ("affy" %in% rownames(installed.packages())){}
+  else {
+    source("https://bioconductor.org/biocLite.R")
+    biocLite(c('mygene','affy'))
+  }
+  if ('data.table' %in% rownames(installed.packages())){}
+  else {
+    install.packages('data.table', repos='http://cran.us.r-project.org')
+  }
+  if ('stringr' %in% rownames(installed.packages())){}
+  else {
+    install.packages('stringr', repos='http://cran.us.r-project.org')
+  }
+  if ('VennDiagram' %in% rownames(installed.packages())){}
+  else {
+    install.packages('VennDiagram', repos='http://cran.us.r-project.org')
+  }
+}
+
+ins_check_run()
+library(data.table)
+library(affy)
+library(stringr)
+library(mygene)
+library(VennDiagram)
+#####
+#data
+
+#We should chat a bit more about using Tukey's and handling 0's/missing values with Brent.
+#Ask me about some updates for doing a bit more filtering of TMT data.
+
+main <- function(peptides_file, db_path) {
+	peptides_file = read.delim(peptides_file,header=TRUE,stringsAsFactors=FALSE,fill=TRUE)
+  peptides_txt = peptides_file
+	intensity_columns = names(peptides_txt[,str_detect(names(peptides_txt),"Intensity\\.*")]) #Pulls out all lines with Intensity in them.
+	intensity_columns = intensity_columns[2:length(intensity_columns)] #Removes the first column that does not have a bait. 
+	peptides_txt_mapped = as.data.frame(map_peptides_proteins(peptides_txt)) #This function as below sets every line to a 1 to 1 intensity to each possible protein.
+	peptides_txt_mapped$Uniprot = str_extract(peptides_txt_mapped$mapped_protein, "[OPQ][0-9][A-Z0-9]{3}[0-9]|[A-NR-Z][0-9]([A-Z][A-Z0-9]{2}[0-9]){1,2}") #Pulls out just Uniprot id from the script.
+	peptides_txt_mapped = subset(peptides_txt_mapped,!is.na(Uniprot)) #removes reverse sequences and any that didn't match a uniprot accession
+	columns_comb = c("Uniprot", intensity_columns) 
+	peptides_mapped_intensity = subset(peptides_txt_mapped, select = columns_comb) #Subsets out only the needed cloumns for Tukeys (Uniprot IDS and baited intensities)
+	swissprot_fasta = scan(db_path, what="character")
+	peptides_txt_mapped_log2 = peptides_mapped_intensity
+  # Takes the log2 of the intensities. 
+	for (i in intensity_columns) { 
+		peptides_txt_mapped_log2[,i] = log2(subset(peptides_txt_mapped_log2, select = i))
+	}
+  #get the minimum from each column while ignoring the -Inf; get the min of these mins for the global min; breaks when there's only one intensity column 
+	global_min = min(apply(peptides_txt_mapped_log2[,2:ncol(peptides_txt_mapped_log2)],2,function(x) {
+	  min(x[x != -Inf])
+	}))
+	peptides_txt_mapped_log2[peptides_txt_mapped_log2 == -Inf] <- 0
+  #uniprot accessions WITHOUT isoforms; it looks like only contaminants contain isoforms anyways
+	mapped_protein_uniprotonly = str_extract(peptides_txt_mapped_log2$Uniprot,"[OPQ][0-9][A-Z0-9]{3}[0-9]|[A-NR-Z][0-9]([A-Z][A-Z0-9]{2}[0-9]){1,2}") 
+	mapped_protein_uniprot_accession = str_extract(peptides_txt_mapped_log2$Uniprot,"[OPQ][0-9][A-Z0-9]{3}[0-9](-[0-9]+)?|[A-NR-Z][0-9]([A-Z][A-Z0-9]{2}[0-9]){1,2}(-[0-9]+)?|[OPQ][0-9][A-Z0-9]{3}[0-9]|[A-NR-Z][0-9]([A-Z][A-Z0-9]{2}[0-9]){1,2}")
+	peptides_txt_mapped_log2$mapped_protein = mapped_protein_uniprotonly
+  # Runs the Tukey function returning completed table
+  peptides_txt_mapped_log2 = subset(peptides_txt_mapped_log2,mapped_protein %in% swissprot_fasta)
+	protein_intensities_tukeys = get_protein_values(peptides_txt_mapped_log2,intensity_columns)
+  protein_intensities_tukeys[protein_intensities_tukeys == 1] <- 0
+  write.table(protein_intensities_tukeys, "./tukeys_output.txt", row.names = FALSE, col.names = TRUE, quote = FALSE, sep = "\t")	
+
+}
+
+map_peptides_proteins = function(peptides_in) {
+    #reverse sequences are blank but have a razor protein indicating that they are reverse; exclude these for now
+    peptides_in = subset(peptides_in,peptides_in$Proteins != "")
+    results_list = list()
+    k = 1
+    for (i in 1:nrow(peptides_in)) {
+        protein_names = peptides_in[i,"Proteins"]
+        protein_names_split = unlist(strsplit(protein_names,";"))
+        for (j in 1:length(protein_names_split)) {
+            peptides_mapped_proteins = data.frame(peptides_in[i,],mapped_protein=protein_names_split[j],stringsAsFactors=FALSE)
+            results_list[[k]] = peptides_mapped_proteins
+            k = k+1
+            
+        }
+    }
+    return(rbindlist(results_list))
+}
+
+get_protein_values = function(mapped_peptides_in,intensity_columns_list) {
+  unique_mapped_proteins_list = unique(mapped_peptides_in$mapped_protein) # Gets list of all peptides listed.
+  # Generates a blank data frame with clomns of Intensities and rows of Uniprots.
+  Tukeys_df = data.frame(mapped_protein = unique_mapped_proteins_list, stringsAsFactors = FALSE ) 
+  for (q in intensity_columns_list) {Tukeys_df[,q] = NA}
+  for (i in 1:length(unique_mapped_proteins_list)) {
+    mapped_peptides_unique_subset = subset(mapped_peptides_in, mapped_protein == unique_mapped_proteins_list[i])
+    #calculate Tukey's Biweight from library(affy); returns a single numeric
+    #results_list[[i]] = data.frame(Protein=unique_mapped_proteins_list[i],Peptides_per_protein=nrow(mapped_peptides_unique_subset))
+    for (j in intensity_columns_list) {
+      #Populates with new Tukeys values.
+      Tukeys_df[i,j] = 2^(tukey.biweight(mapped_peptides_unique_subset[,j]))
+    }
+  }
+  return(Tukeys_df)
+}
+
+
+args <- commandArgs(trailingOnly = TRUE)
+main(args[1], args[2])