changeset 2:2843d0da7f20 draft

Uploaded

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/nsaf_scoring.R	Wed May 11 10:51:19 2016 -0400
@@ -0,0 +1,80 @@
+###################################################################################################
+# R-code: APOSTL Global Variables
+# Author: Brent Kuenzi
+
+###################################################################################################
+# This program performs the file merging as well as a serious of calculations
+# Following merging the following parameters will be calculated:
+# 1) CRAPomePCT
+# 2) NSAF
+# 3) NSAFscore
+# The resulting table will be exported. This is performed as its own tool and should not be used
+# for input into the interactive analysis tool or the standalone bubble graph tool
+################################## Dependencies ###################################################
+library(dplyr); library(tidyr)
+################################# Read in Data ####################################################
+## REQUIRED INPUTS ##
+## 1) listfile (filename)
+#listfile <- "EGFR_list.txt"
+## 2) Prey File (filename)
+#preyfile <- "EGFR_prey.txt"
+## 3) crapome File (filename or FALSE)
+#crapfile <- "EGFR_crap.txt"
+## 4) Inter File (filename)
+#interfile <- "inter.txt"
+################################# Create Table ####################################################
+merge_files <- function(SAINT_DF, prey_DF, crapome=FALSE) {
+  SAINT <- read.table(SAINT_DF, sep='\t', header=TRUE)
+  prey <- read.table(prey_DF, sep='\t', header=FALSE); colnames(prey) <- c("Prey", "Length", "PreyGene")
+  DF <- merge(SAINT,prey)
+  
+  if(crapome!=FALSE) {
+    crapome <- read.table(crapome, sep='\t', header=TRUE)
+    colnames(crapome) <- c("Prey", "Symbol", "Num.of.Exp", "Ave.SC", "Max.SC")
+    DF1 <- merge(DF, crapome); as.character(DF1$Num.of.Exp); DF1$Symbol <- NULL;
+    DF1$Ave.SC <- NULL; DF1$Max.SC <- NULL #remove unnecessary columns
+    DF1$Num.of.Exp <- sub("^$", "0 / 1", DF1$Num.of.Exp ) #replace blank values with 0 / 1
+    DF <- DF1 %>% separate(Num.of.Exp, c("NumExp", "TotalExp"), " / ") #split into 2 columns
+    DF$CrapomePCT <- round(100 - (as.integer(DF$NumExp) / as.integer(DF$TotalExp) * 100), digits=2) #calculate crapome %
+    
+  }
+  DF$FoldChange <- round(log2(DF$FoldChange),digits=2)
+  colnames(DF)[(colnames(DF)=="FoldChange")] <- "log2(FoldChange)"
+  
+  DF$SAF <- DF$AvgSpec / DF$Length
+  by_bait <-  DF %>% group_by(Bait) %>% mutate("NSAF" = SAF/sum(SAF))
+  by_bait$SAF <- NULL
+  return(by_bait[!duplicated(by_bait),])
+}
+
+main <- function(listfile, preyfile, crapfile, interfile) {
+  working <- as.data.frame(merge_files(listfile, preyfile, crapfile))
+  inter_df <- read.table(interfile, sep='\t', header=FALSE)
+  working$temp <- strsplit(as.character(working$ctrlCounts),"[|]")
+  cnt <- 0
+  for(i in working$temp){
+    cnt <- cnt+1
+    working$ctrl_mean[cnt] <- mean(as.numeric(unlist(i)))
+    working$ctrl_number[cnt] <- length(i)}
+  working$ctrl_SAF <- working$ctrl_mean / working$Length
+  main.data <-  working %>% group_by(Bait) %>% mutate("control_NSAF" = ctrl_SAF/sum(ctrl_SAF))
+  ctrl_SAF_constant <- 1/mean(main.data$ctrl_SAF)
+  # add ctrl_SAF_constant to prevent dividing by 0
+  cnt <- 0
+  for(i in main.data$control_NSAF){
+    cnt <- cnt + 1
+    main.data$nsafScore[cnt] <- ((main.data$NSAF[cnt])+ctrl_SAF_constant)/((i/main.data$ctrl_number[cnt])+ctrl_SAF_constant)
+  }
+  main.data$NSAF <- log(main.data$NSAF)
+  main.data$nsafScore <- log(main.data$nsafScore)
+  main.data <- filter(main.data, NSAF > -Inf)
+  colnames(main.data)[colnames(main.data)=="NSAF"] <- "ln(NSAF)"
+  colnames(main.data)[colnames(main.data)=="nsafScore"] <- "NSAFScore"
+  main.data$SAF <- NULL; main.data$ctrl_SAF <- NULL
+  main.data$control_NSAF <- NULL; main.data$temp <- NULL
+  main.data$ctrl_mean <- NULL
+  write.table(main.data,file="SaintTable.txt",sep="\t",row.names=FALSE,quote=FALSE)
+}
+
+args <- commandArgs(trailingOnly = TRUE)
+main(args[1], args[2], args[3], args[4])