doc

bin/GOBarplot.R

+##NAME = "GOBarplot.R"
+##SYNOPSIS = "GOBarplot.R |-f "file1,file2..." --names "fileName1,fileName2..." --fileFormat "topGO" or "twoColumns" -o <results_path>"
+##EXAMPLE = "Rscript --vanilla GOBarplot.R -f "./data/file1,./data/file2" --names "fileName1,fileName2" --fileFormat "topGO" -o "./results""
+##DATE = "03/2016"
+##AUTHORS = "Gaëlle Lefort"
+##KEYWORDS = "RNAseq gene ontology barplot"
+##DESCRIPTION = "GOEnrichment.R carries out a barplot to compare gene ontology between multiple set of files." 
+
+
 ############################# Enrichment analysis ##############################
 ################################################################################
 
@@ -43,8 +52,7 @@ option_list = list(
               metavar = "character")
   ); 
 
-opt_parser = OptionParser(usage="Perform an enrichment analysis for 
-                          Gene Ontology (GO)", option_list = option_list);
+opt_parser = OptionParser(usage="Carries out a barplot to compare gene ontology between multiple set of files", option_list = option_list);
 opt = parse_args(opt_parser);
 
 ##############

bin/GOEnrichment.R

+##NAME = "GOEnrichment.R"
+##SYNOPSIS = "GOEnrichment.R |-f <raw_data_path>/<file_name>.csv --fileFormat "topGO" or "twoColumns" --interest <interest_data_path>/<interest_file_name>.csv -o <results_path> --test "fisher" or "ks" --algorithm "classic", "elim" or "weight" --paramAlgo "bonferroni", "BH", 0.01, 0.05, "ratio" or "log" --alpha 0.05 --target "contigs", "gene"..."
+##EXAMPLE = "Rscript --vanilla GOEnrichment.R --file "./data/topGO.csv" --fileFormat "topGO" --interest "./data/gene.txt" --out "./results/" --test "fisher" --algorithm "elim" --paramAlgo 0.01 --alpha 0.05 --target "contigs""
+##DATE = "03/2016"
+##AUTHORS = "Gaëlle Lefort"
+##KEYWORDS = "RNAseq GO enrichment"
+##DESCRIPTION = "GOEnrichment.R perform an enrichment analysis for Gene Ontology (GO)." 
+
+
 ############################# Enrichment analysis ##############################
 ################################################################################
 
@@ -10,7 +19,7 @@ packages <- c("optparse", # to read arguments from a command line
 for(package in packages){
   # if package is installed locally, load
   if (!(package %in% rownames(installed.packages()))) {
-    install.packages(package, repos="http://cran.univ-paris1.fr")
+    install.packages(package)
   }
   do.call('library', list(package))
 } 
@@ -18,7 +27,7 @@ for(package in packages){
 #Bioconductor package
 if (!("topGO" %in% rownames(installed.packages()))) {
   source("http://www.bioconductor.org/biocLite.R")
-  biocLite("topGO")
+  biocLite("topGO", suppressUpdates = TRUE, suppressAutoUpdate = TRUE, ask = FALSE)
 }
 library(topGO) # GO enrichment
 
@@ -80,9 +89,9 @@ opt = parse_args(opt_parser);
 #opt$out <- XXX # for example "C:/My documents/results"
 #opt$test <- XXX # "fisher" or "KS"
 #opt$algorithm <- XXX # ('classic', 'elim' or 'weight')
-#opt$paramAlgo <- XXX # ('bonferroni' or 'BH')
+#opt$paramAlgo <- XXX # ('bonferroni' or 'BH' for classic, 0.01 for elim and 'ratio' or 'log' for weight)
 #opt$alpha <- 0.05 # for example 0.05
-#opt$target <- "contigs" # for example contigs
+#opt$target <- "contigs" # for example contigs, gene...
 
 
 # table with genes and GO, genes of interest, test and algorithm are needed to 
@@ -114,6 +123,34 @@ if(is.null(opt$paramAlgo)){
   }
 }
 
+if(opt$algorithm == "classic" & !(opt$paramAlgo == "bonferroni" | opt$paramAlgo == "BH")){
+  stop("paramAlgo need to be equals to 'bonferroni' or 'BH'\n", 
+       call. = FALSE)
+}
+
+if(opt$algorithm == "classic" & !(opt$paramAlgo == "bonferroni" | opt$paramAlgo == "BH")){
+  stop("paramAlgo need to be equals to 'bonferroni' or 'BH'\n", 
+       call. = FALSE)
+}
+
+
+if(opt$algorithm == "elim"){
+  opt$paramAlgo <- as.numeric(opt$paramAlgo)
+  if(is.na(opt$paramAlgo)){
+    stop("paramAlgo need to be a number\n", 
+         call. = FALSE)
+  }
+  if(opt$paramAlgo > 1){
+    stop("paramAlgo need to be inferior to 1\n", 
+         call. = FALSE)
+  }
+}
+
+if(opt$algorithm == "weight" & !(opt$paramAlgo == "ratio" | opt$paramAlgo == "log")){
+  stop("paramAlgo need to be equals to 'ratio' or 'log'\n", 
+       call. = FALSE)
+}
+
 
 #####################################################
 ### ---------------------Input data and preprocessing
@@ -299,10 +336,10 @@ for(ontology in c("BP", "MF", "CC")){
     resultTest@score <- p.adjust(resultTest@score, method = opt$paramAlgo)
   } else if (opt$algorithm == "elim"){
     resultTest <- runTest(myGOdata, algorithm = opt$algorithm, statistic = opt$test, 
-                          cutOff = as.numeric(opt$cutOff))
+                          cutOff = as.numeric(opt$paramAlgo))
   } else if (opt$algorithm == "weight"){
     resultTest <- runTest(myGOdata, algorithm = opt$algorithm, statistic = opt$test, 
-                          sigRatio = opt$weightFunc)
+                          sigRatio = opt$paramAlgo)
   }
   
   sigRes <- resultTest@score[resultTest@score <= opt$alpha]
@@ -328,7 +365,9 @@ for(ontology in c("BP", "MF", "CC")){
   
 }
 
-names(GOgeneSig)[4] <- opt$target 
+if(!is.null(GOgeneSig)){
+  names(GOgeneSig)[4] <- opt$target 
+}
 write.table(GOgeneSig, file = normalizePath(file.path(opt$out, 
                                                      paste0("GOgeneSig.csv")), 
                                            mustWork = FALSE), sep = "\t", 
@@ -342,7 +381,7 @@ write.table(unique(GOgeneSig[,c("ontology", "GO", "GODef", "pval")]),
 
 
 ## JSON
-stat <- list("notInTheAnalysis" = ifelse(!is.na(notInAnalysis[1]), notInAnalysis, "none"))
+stat <- list("notInTheAnalysis" = ifelse(!is.na(notInAnalysis[1]), as.character(notInAnalysis), "none"))
 
 write(gsub(" ", "", toJSON(list(stat=stat), collapse = "")), 
       file = normalizePath(file.path(opt$out, "results.json"), 

bin/Normalization.R

+##NAME = "Normalization.R"
+##SYNOPSIS = "Normalization.R |-f <raw_data_path>/<file_name>.csv -o <results_path>"
+##EXAMPLE = "Rscript --vanilla Normalization.R --file './data/count_table.csv' --out './results/'"
+##DATE = "03/2016"
+##AUTHORS = "Gaëlle Lefort"
+##KEYWORDS = "RNAseq normalization"
+##DESCRIPTION = "Normalization.R imports data, converts them into a DGEList object (edgeR), does all normalization methods and produces diagnostic plots." 
+
+
 ################################ Normalization #################################
 ################################################################################