add Guitar

src/R/diff_methyl.R

@@ -11,11 +11,23 @@ rm(list=ls())                 # remove all the objects from the R session
 general_path <- "/Users/cbecavin/Documents/m6aAkker/"
 #general_path <- "/pasteur/projets/policy01/m6aAkker/"
 
-project_name <- "LivOld"
-peak_name <- "LivOld"
+# expr1 = read.delim(file="GSM462282_exp.txt")
+# expr2 = read.delim(file="GSM462283_exp.txt")
+# expr3 = read.delim(file="GSM462284_exp.txt")
+# expr<- merge(expr1,expr2,by = "ID",all = TRUE)
+# expr<- merge(expr,expr3,by = "ID",all = TRUE)
+# expr$'Am_vs_GF' = expr$Am - expr$GF
+# expr$'Plant_vs_GF' = expr$Plant - expr$GF
+# expr$'Plant_vs_Am' = expr$Plant - expr$Am
+# affy_probe = read.delim(file="Affy_probes.txt")
+# final <- merge(expr,affy_probe, by.all="ID", all = TRUE)
+# write.table(final,file="GEO_diff_exp_annot.txt",sep="\t",quote=FALSE,row.names = FALSE)
+
+project_name <- "CecAm"
+peak_name <- "CecAm"
 project_dir <- paste(general_path,"PeakDiffExpression/",project_name,"/",sep="")
 annotation_name <- "gencode.vM13"
-exp_design_name <- "LivOld"
+exp_design_name <- "CecAm"
 exp_design_file = paste(project_dir,"/../../ExpDesign/",exp_design_name,"_exp_design.txt",sep="")
 
 #rscript_folder <- "/pasteur/projets/policy01/m6aAkker/MeRIPSeq/src/R/"
@@ -78,7 +90,7 @@ save_contrast()
 diff_summary()
 
 # # Do GUITAR plot (long execution time)
-#guitar_plot()
+guitar_plot()
 
 # Plot PCA and Heatmap of differentially methylated sites
 filter_table <- data.frame(norm_voom_epi[diff_peaks,])

src/R/guitar_plot.R

@@ -5,13 +5,13 @@ guitar_plot <- function(){
   # Init Guitar plot
   print("Init GUITAR plot")
   guitar_file <-paste("../../temp/",annotation_name,"_guitar.RData",sep="")
-  if(!file.exists(guitar_file)){
+  #if(!file.exists(guitar_file)){
     gencodeVM13 <- makeTxDbFromGFF(paste("../../Genome/",annotation_name,".annotation.gtf",sep=""),format = "gtf")
     gc_mm10_txdb <- makeGuitarCoordsFromTxDb(gencodeVM13)
     save(gc_mm10_txdb,file = guitar_file)
-  }else{
-    load(guitar_file)
-  }
+  #}else{
+  #  load(guitar_file)
+  #}
   
   # Set data for Guitar plot
   list_name <- list("","_Meth","_Meth_Epi","_MethGene","_MethNoGene")