Feat: Add peak analysis script to pipe4C

pipe4C/Dockerfile

@@ -3,7 +3,7 @@ FROM r-base:3.6.2
 RUN apt-get update && apt-get install -y git libcurl4-gnutls-dev libxml2-dev libssl-dev bowtie2 samtools
 # Install R packages
 RUN mkdir /RScripts
-ADD install.R conf_generator.R /RScripts/
+ADD install.R conf_generator.R peak_analysis.R /RScripts/
 RUN Rscript /RScripts/install.R
 # Clone pipe4C
 ENV PIPE4C_REPO=https://github.com/deLaatLab/pipe4C.git \

pipe4C/peak_analysis.R

@@ -0,0 +1,35 @@
+# Load peakC and pipe4C functions
+library(peakC)
+source("/RScripts/pipe4C/functions.R")
+
+# Get rds file names
+getRDSFileNames <- function() {
+  args <- commandArgs(TRUE)
+  return(list(path = args[1], fileNames = list.files(args[1])))
+}
+
+mkDir <- function(path) {
+  folders <- strsplit(path, "/")[[1]]
+  resFolder <- folders[length(folders)-1]
+  dir.create(resFolder)
+  return(resFolder)
+}
+
+doIndividualPeakAnalysis <- function(RDSpath, RDSFileNames, resFolder) {
+  for (f in RDSFileNames) {
+    print(paste("Run PeakC analysis for", f))
+    results <- doPeakC(rdsFiles = paste0(RDSpath, "/", f))
+    name <- sub(".rds", "", f)
+    ymax <- c(10, 100, 1000)
+    for (y in ymax) {
+      pdf(paste0(resFolder, "/", name, "_peak_plot_", y, ".pdf"))
+      plot_C(results, y.max=y)
+      dev.off()
+    }
+    exportPeakCPeaks(resPeakC=results,bedFile=paste0(resFolder, "/", name, "_peakC_peaks.bed"),name=name)
+  }
+}
+
+RDSInfo <- getRDSFileNames()
+RDSInfo$resFolder <- mkDir(RDSInfo$path)
+doIndividualPeakAnalysis(RDSInfo$path, RDSInfo$fileNames, RDSInfo$resFolder)