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Commit fbe7f857 authored by Christophe  BECAVIN's avatar Christophe BECAVIN
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Update diff_meth.R by removing RNA_IP management

parent 9e26d933
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......@@ -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"))
......@@ -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="""
......
......@@ -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)
}
......
......@@ -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="")
......
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