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Commit dbc973de authored by Christophe  BECAVIN's avatar Christophe BECAVIN
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add Guitar

parent 28481998
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......@@ -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,])
......
......@@ -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")
......
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