# HG changeset patch
# User cs76
# Date 1449486353 18000
# Node ID c403de9adce740b22ef2ead08ea7ce900f5995a9
# Parent 5cd5308cc3981eae2aa17d4cc60a322f6b6438f8
Uploaded
diff -r 5cd5308cc398 -r c403de9adce7 ipo.R
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/ipo.R Mon Dec 07 06:05:53 2015 -0500
@@ -0,0 +1,53 @@
+args<-commandArgs(TRUE)
+
+workingDirectory<-args[3]
+logFile<-paste(workingDirectory,'/run.log', sep='')
+graphsDirectory<-paste(workingDirectory,'/graphs', sep='')
+outputCSV<-paste(workingDirectory,'/IPO_PP.csv', sep='')
+
+dir.create(workingDirectory)
+zz <- file(logFile, open="wt")
+sink(zz)
+sink(zz, type="message")
+
+library("xtable")
+library(IPO)
+#print(args)
+
+peakpickingParameters <- getDefaultXcmsSetStartingParams('centWave')
+#setting levels for min_peakwidth to 10 and 20 (hence 15 is the center point)
+peakpickingParameters$min_peakwidth <- c(10,20)
+peakpickingParameters$max_peakwidth <- c(26,42)
+#setting only one value for ppm therefore this parameter is not optimized
+peakpickingParameters$ppm <- 20
+peakpickingParameters$nSlaves <- 4 # as.numeric(args[3])
+type <- "centWave"
+
+resultPP <- optimizeXcmsSet(files=args[1], params=peakpickingParameters, nSlaves=4, subdir=graphsDirectory)
+
+print (resultPP)
+
+graphs<-""
+for(i in 1:(length(resultPP)-1))
+{
+ graphs<-paste(graphs,"![](graphs/rsm_", i ,".jpg)
",sep='')
+}
+
+list <- c(resultPP$best_settings$parameters, as.list(resultPP$best_settings$result), list(type=type))
+table <- print(xtable(t(data.frame(list))), type = "html")
+write.csv(c(resultPP$best_settings$parameters, as.list(resultPP$best_settings$result), list(type=type)),file=outputCSV)
+
+html<-paste('
+
+
+
+
+
+ ', sep='')
+
+fileConn<-file(args[2])
+writeLines(html, fileConn)
+close(fileConn)
+
+sink(type = "message")
+sink()
\ No newline at end of file