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diffBind_analysis.R

+# Packages -------
+library(DiffBind)
+library(tidyverse)
+library(rtracklayer)
+
+
+# input file
+samples <- read.csv2("sampleSheetCons.csv")
+
+
+DBdata <- dba(sampleSheet = samples, config = list(doBlacklist = FALSE, doGreylist = FALSE, RunParallel = FALSE))
+
+# applicate the greyList
+greyList <- import.bed("gl.bed")
+DBdata <- dba.blacklist(DBdata, greylist = greyList)
+
+#dba count
+db <- dba.count(DBdata, summits = FALSE)
+
+saveRDS(db, "dbCountCons.RDS")
+
+#-----------------
+
+dbaCount <- readRDS("dbCountCons.RDS")
+
+info <- dba.show(dbaCount)
+
+libsizes <- cbind(LibReads=info$Reads, FRiP=info$FRiP, PeakReads=round(info$Reads * info$FRiP))
+rownames(libsizes) <- info$ID
+
+png("dbaCount.png")
+plot(dbaCount)
+dev.off()
+
+#Normalizing the data
+result <- dba.normalize(dbaCount)
+
+#Establishing a model design and contrast 
+# TODO reordonner la ligne
+result <- dba.contrast(dbaCount, reorderMeta=list(Condition="fasted"))
+
+
+ #Performing the differential analysis
+result <- dba.analyze(result)
+dba.show(result, bContrasts=TRUE)
+png("diff_an_dba_cpg.png")
+plot(result, contrast=1)
+dev.off()
+
+
+#Retrieving the differentially bound sites
+result.DB_line <- dba.report(result, contrast = 1)
+result.DB_cons <- dba.report(result, contrast = 2)
+
+
+saveRDS(result.DB_line, "dba_report_Cons_line.RDS")
+saveRDS(result.DB_cons, "dba_report_cons_cond.RDS")
+
+
+
+# Plotting in DiffBind
+png("dba_ven_line_con3.png")
+dba.plotVenn(result, bDB=TRUE, bGain=TRUE, bLoss=TRUE)
+dev.off()
+
+png("dba_PCA_line_cons2.png")
+dba.plotPCA(result, contrast=2, label=DBA_FACTOR)
+dev.off()
+
+
+png("dba_plot_cobs.png")
+dba.plotMA(result)
+dev.off()
+
+
+
+png("dba_volcano_cons.png")
+dba.plotVolcano(result)
+dev.off()
+
+
+png("dba_boxplot_cons.png")
+pvals <- dba.plotBox(result)
+dev.off()
+
+
+hmap <- colorRampPalette(c("magenta", "white", "blue"))(n = 13)
+png("dba_heatMap_cpg.png")
+readscores <- dba.plotHeatmap(result, contrast=1, correlations=FALSE, scale="row", colScheme = hmap)
+dev.off()