public override IEnumerable <string> Process()
{
Progress.SetMessage("filter process started at {0}", DateTime.Now);
var watch = new Stopwatch();
watch.Start();
var tsvfile = _options.OutputFile + ".rtsv";
var roptions = new RProcessorOptions()
{
RExecute = _options.GetRCommand(),
RFile = _options.TargetRFile,
ExpectResultFile = _options.ROutputFile
};
new RProcessor(roptions).Process();
if (!File.Exists(_options.ROutputFile))
{
throw new Exception(string.Format("R command failed, look at the file {0}!\nMake sure that your R and R packages brglm, stringr have been installed.", roptions.RFile + ".log"));
}
else if (!_options.IsValidation)
{
var items = new FilterItemTextFormat().ReadFromFile(_options.ROutputFile);
var unfilteredfile = Path.ChangeExtension(_options.ROutputFile, ".vcf");
new FilterItemVcfWriter(_options).WriteToFile(unfilteredfile, items);
items.RemoveAll(m => !m.Filter.Equals("PASS"));
var vcfFile = Path.ChangeExtension(_options.OutputFile, ".vcf");
new FilterItemVcfWriter(_options).WriteToFile(vcfFile, items);
new FilterItemTextFormat().WriteToFile(_options.OutputFile, items);
}
watch.Stop();
Progress.SetMessage("filter process ended at {0}, cost {1}", DateTime.Now, watch.Elapsed);
return(new[] { _options.OutputFile });
}
public void Calculate(IsobaricResult ir, string tempFilename)
{
if (!this.performPurityCorrection && !this.performGraph)
{
return;
}
tempFilename = tempFilename.Replace("\\", "/");
var dataFile = tempFilename + ".data";
using (var sw = new StreamWriter(dataFile))
{
sw.WriteLine("Scan\t{0}", (from c in used select c.Name).Merge("\t"));
foreach (var ii in ir)
{
sw.WriteLine("{0}\t{1}", ii.Scan.Scan, (from rep in ii.Reporters select string.Format("{0:0.##}", rep.Intensity)).Merge("\t"));
}
}
var purityFile = tempFilename + ".purity";
using (var sw = new StreamWriter(purityFile))
{
var purity = plexType.IsotopicTable;
sw.WriteLine("Channel\t{0}", (from c in used select c.Name).Merge("\t"));
for (int i = 0; i < used.Count; i++)
{
sw.Write(used[i].Name);
for (int j = 0; j < used.Count; j++)
{
sw.Write("\t{0:0.####}", purity[used[i].Index, used[j].Index] / 100);
}
sw.WriteLine();
}
}
var rfile = tempFilename + ".r";
var pngFile = tempFilename + ".png";
using (var sw = new StreamWriter(rfile))
{
sw.WriteLine(@"
data<-read.table(""" + dataFile + @""", header=T, row.names=1)
");
if (this.performPurityCorrection)
{
sw.WriteLine(@"
library(nnls)
table<-read.table(""" + purityFile + @""", header=T, row.names=1)
m<-as.matrix(table)
m=t(m)
correctedData<-apply(data, 1, function(x){
v<-nnls(m, x)
v$x
})
correctedData<-t(correctedData)
colnames(correctedData)<-colnames(data)
data<-data.frame(correctedData)
");
}
sw.WriteLine(@"
write.csv(data, file=""" + tempFilename + @""")
");
if (this.performGraph)
{
sw.WriteLine(@"
dd<-data.frame(data)
png(""" + pngFile + @""",
width=1000 * ncol(dd), height=1000*ncol(dd), res=300)
split.screen(c(ncol(dd),ncol(dd)))
id<-0
cols<-rainbow(ncol(dd))
for(i in c(1:ncol(dd))){
for(j in c(1:ncol(dd))){
id<-id+1
screen(id)
if(i == j){
dl<-list()
maxy<-0
for(k in c(1:ncol(dd))){
if(k != i){
notZero<-dd[,i] > 0 & dd[,k] > 0
xx<-dd[notZero,i]
yy<-dd[notZero,k]
r<-log2(yy/xx)
d<-density(r)
dl[[colnames(dd)[k]]]<-d
maxy<-max(maxy, max(d$y))
}
}
maxy<-floor(maxy) + 1
s<-0
for(k in c(1:ncol(dd))){
if(k != i){
s<-s+1
if(s == 1){
par(mar=c(2,2,3,2), new=TRUE)
plot(dl[[colnames(dd)[k]]], xlim=c(-2,2), ylim=c(0,maxy), xlab="""", col=cols[k], main=colnames(dd)[i])
}else{
lines(dl[[colnames(dd)[k]]], col=cols[k])
}
}
}
}else{
notZero<-dd[,i] > 0 & dd[,j] > 0
xx<-dd[notZero,i]
yy<-dd[notZero,j]
m<-log2(yy/xx)
a<-log2((yy+xx)/2)
par(mar=c(2,2,3,2), new=TRUE)
plot(x=a, y=m, col=cols[j],xlab="",ylab="",main=paste0(colnames(dd)[j], ""/"", colnames(dd)[i]), cex=0.1, pch=20, xlim=c(10,30), ylim=c(-5,5))
abline(a=0, b=0)
}
}
}
close.screen()
dev.off()
");
}
}
var roptions = new RProcessorOptions()
{
RExecute = rExecute,
RFile = rfile,
ExpectResultFile = tempFilename
};
new RProcessor(roptions).Process();
if (!File.Exists(tempFilename))
{
throw new Exception(string.Format("Purity correction failed!\nMake sure that your R and R packages nnls, limma have been installed.\nOtherwise, send those three files to [email protected]\n{0}\n{1}\n{2}",
dataFile,
purityFile,
rfile));
}
//read back all corrected intensities
using (var sr = new StreamReader(tempFilename))
{
var line = sr.ReadLine();
var index = 0;
while ((line = sr.ReadLine()) != null)
{
if (string.IsNullOrWhiteSpace(line))
{
break;
}
var parts = line.Split(',');
for (int i = 1; i < parts.Length; i++)
{
ir[index][i - 1].Intensity = double.Parse(parts[i]);
}
index++;
}
}
//File.Delete(dataFile);
//File.Delete(purityFile);
//File.Delete(rfile);
//File.Delete(tempFilename);
}
