Update diff_meth.R by removing RNA_IP management

INSTALL.txt

@@ -76,11 +76,9 @@ conda install bioconductor-biomart
 conda install bioconductor-edger
 conda install bioconductor-genomicfeatures
 
-
-
 conda install r-sartools
 conda install bioconductor-sva
 # in R
 install.packages(c("ggplot2","gplots","ggfortify","RColorBrewer","seqinr","dendextend"))
-
+install.packages(c("pheatmap","GGally"))
 

src/bash_slurm/RunDiffMeth.sh

@@ -19,8 +19,8 @@ file_name=${exp_design_name}_${bed_name}
 if [ ! -d $folder/temp/${SLURM_JOB_NAME} ]; then
 	mkdir $folder/temp/${SLURM_JOB_NAME}
 fi
-shFile=/pasteur/projets/policy01/m6aAkker/temp/${SLURM_JOB_NAME}/${file_name}_${SLURM_JOB_NAME}.sh
-logFile=/pasteur/projets/policy01/m6aAkker/temp/${SLURM_JOB_NAME}/${file_name}_${SLURM_JOB_NAME}.log
+shFile=/pasteur/projets/policy01/m6aAkker/temp/${SLURM_JOB_NAME}/${file_name}_${SLURM_JOB_NAME}_${SLURM_JOB_ID}.sh
+logFile=/pasteur/projets/policy01/m6aAkker/temp/${SLURM_JOB_NAME}/${file_name}_${SLURM_JOB_NAME}_${SLURM_JOB_ID}.log
 
 # Create script SH to run in qsub
 scriptSH="""

src/diff_methyl.R

@@ -59,6 +59,8 @@ if(file.exists(rdata_file)){
     color_biocond <- c("seagreen4","seagreen3","gray0","gray51","tan4","tan3","firebrick1")
   }else if(exp_design_name == "LivOld"){
     color_biocond <- c("seagreen4","gray0","dodgerblue","tan4")
+  }else{
+    color_biocond <- c("seagreen4","seagreen3","gray0","gray51","tan4","tan3","firebrick1")
   }
 
   init_parameters()
@@ -103,9 +105,9 @@ if(file.exists(rdata_file)){
   filter_table <- data.frame(norm_voom_epi[diff_peaks,])
   plot_heatmap(filter_table,"")
   plot_pca(filter_table,"")
-  filter_table <- filter_table[,colnames(filter_table) %in% colnames(counts_RNA_IP)]
-  plot_heatmap(filter_table,"_IP")
-  plot_pca(filter_table,"_IP")
+  #filter_table <- filter_table[,colnames(filter_table) %in% colnames(counts_RNA_IP)]
+  #plot_heatmap(filter_table,"_IP")
+  #plot_pca(filter_table,"_IP")
   filter_table <- data.frame(norm_voom_epi[diff_peaks,])
   filter_table <- filter_table[,colnames(filter_table) %in% colnames(counts_RNA_I)]
   plot_heatmap(filter_table,"_Input")
@@ -114,6 +116,8 @@ if(file.exists(rdata_file)){
   plot_heatmap(filter_table,"_Gene")
   plot_pca(filter_table,"_Gene")
 
+  print("Save RData")
+  print(rdata_file)
   save.image(rdata_file)
 }
 

src/m6aAnalysis/R/plot_description.R

@@ -23,18 +23,18 @@ plot_description <- function(){
   }
   write.table( counts_RNA_I[order(counts_RNA_I[,1],decreasing = TRUE)[1:50],], file=paste(image_folder, peak_name,"_Count_RNA_Input.xls",sep=""), quote=FALSE, row.names = FALSE, sep = "\t")
 
-  majSequences <- descriptionPlots(counts=counts_RNA_IP, group=target_RNA_IP[,varInt], col=color_biocond)
-  image_folder = paste(project_dir,"FiguresRNAIP/",sep="")
-  if (!dir.exists(image_folder)){
-    file.rename(from="figures/",to=image_folder)
-  }else{
-    unlink(image_folder, recursive=TRUE)
-    file.rename(from="figures/",to=image_folder)
-  }
-  write.table( counts_RNA_IP[order(counts_RNA_IP[,1],decreasing = TRUE)[1:50],], file=paste(image_folder, peak_name,"_Count_RNA_IP.xls",sep=""), quote=FALSE, row.names = FALSE, sep = "\t")
-  if (!dir.exists(figure_folder)){
-    dir.create(figure_folder)
-  }
+  # majSequences <- descriptionPlots(counts=counts_RNA_IP, group=target_RNA_IP[,varInt], col=color_biocond)
+  # image_folder = paste(project_dir,"FiguresRNAIP/",sep="")
+  # if (!dir.exists(image_folder)){
+  #   file.rename(from="figures/",to=image_folder)
+  # }else{
+  #   unlink(image_folder, recursive=TRUE)
+  #   file.rename(from="figures/",to=image_folder)
+  # }
+  # write.table( counts_RNA_IP[order(counts_RNA_IP[,1],decreasing = TRUE)[1:50],], file=paste(image_folder, peak_name,"_Count_RNA_IP.xls",sep=""), quote=FALSE, row.names = FALSE, sep = "\t")
+  # if (!dir.exists(figure_folder)){
+  #   dir.create(figure_folder)
+  # }
 
   # majSequences <- descriptionPlots(counts=counts_Trans_I, group=target_RNA_I[,varInt], col=color_biocond)
   # image_folder = paste(project_dir,"FiguresTranscrI/",sep="")