--- a/qualityControl.R	Tue Oct 25 14:41:32 2016 -0400
+++ b/qualityControl.R	Tue Oct 25 14:41:59 2016 -0400
@@ -6,8 +6,7 @@
 # owner : IRRI
 #
 ########################################################
-log <- file(paste(getwd(), "log_QC.txt", sep="/"), open = "wt")
-sink(file = log, type="message")
+
 #######################################################
 dataStats.nbNA <- function(x) {
   return(length(x[is.na(x)]))
@@ -32,6 +31,7 @@
 createReport <- function(genoFile, freqFile, hweFile, out="report.txt") {
   # get basic statistics (nb markers, nb samples, nb NA)
   data <- read.table(genoFile, sep="\t", h=T)
+  missingData <- dataStats.nbNA(data)/length(data)
   dataDimension <- dataStats.matrixSize(data)
   # get MAF info
   freq <- parseFrq(freqFile)
@@ -42,7 +42,8 @@
   # write report
   write(paste("number of marker :", dataDimension$nbMarker), file=out)
   write(paste("number of sample :", dataDimension$nbSample), file=out, append = T)
-  write.table(info, file=out, append = T)
+  write(paste("ratio of missing data :", missingData), file=out, append = T)
+  suppressWarnings(suppressMessages(write.table(info, file=out, append = T)))
 }
 ############################ main ##########################
 cmd <- commandArgs(T)