public override IEnumerable <string> Process()
{
using (var file = new PlinkBedRandomFile(_options.InputFile)
{
Progress = this.Progress
})
{
var locusList = file.Data.Locus;
var individualList = file.Data.Individual;
Progress.SetRange(0, locusList.Count);
for (int i = 0; i < locusList.Count; i++)
{
Progress.SetPosition(i);
var locus = locusList[i];
var data = file.Read(locus.MarkerId);
int count1 = 0;
int count2 = 0;
int validSample = 0;
for (int j = 0; j < individualList.Count; j++)
{
if (PlinkData.IsMissing(data[0, j], data[1, j]))
{
continue;
}
validSample++;
if (data[0, j])
{
count2++;
}
else
{
count1++;
}
if (data[1, j])
{
count2++;
}
else
{
count1++;
}
}
locus.Allele1Frequency = ((double)(count1)) / (count1 + count2);
locus.TotalSample = individualList.Count;
locus.ValidSample = validSample;
}
PlinkLocus.WriteToFile(_options.OutputFile, locusList, false, true, true);
}
return(new string[] { _options.OutputFile });
}
public override IEnumerable <string> Process()
{
Progress.SetMessage("Reading data from " + _options.InputFile + "...");
var data = _options.GetFileReader().ReadFromFile(_options.InputFile);
var locusList = data.Locus;
var individualList = data.Individual;
for (int i = 0; i < locusList.Count; i++)
{
var locus = locusList[i];
int count1 = 0;
int count2 = 0;
int validSample = 0;
for (int j = 0; j < individualList.Count; j++)
{
if (data.IsMissing(i, j))
{
continue;
}
validSample++;
if (data.IsHaplotype1Allele2[i, j])
{
count2++;
}
else
{
count1++;
}
if (data.IsHaplotype2Allele2[i, j])
{
count2++;
}
else
{
count1++;
}
}
locus.Allele1Frequency = ((double)(count2)) / (count1 + count2);
locus.TotalSample = individualList.Count;
locus.ValidSample = validSample;
}
PlinkLocus.WriteToFile(_options.OutputFile, locusList, false, true);
return(new string[] { _options.OutputFile });
}
public override IEnumerable <string> Process()
{
var locusList = new List <PlinkLocus>();
using (var sr = new StreamReader(_options.InputFile))
{
string line;
while ((line = sr.ReadLine()) != null)
{
var parts = line.Split(' ');
var locus = new PlinkLocus()
{
Chromosome = int.Parse(parts[0]),
MarkerId = parts[1],
PhysicalPosition = int.Parse(parts[2]),
Allele1 = parts[3],
Allele2 = parts[4]
};
locusList.Add(locus);
var count1 = 0;
var count2 = 0;
for (int i = 5; i < parts.Length; i += 3)
{
if (parts[i].Equals("1"))
{
count1 += 2;
}
else if (parts[i + 1].Equals("1"))
{
count1++;
count2++;
}
else if (parts[i + 2].Equals("1"))
{
count2 += 2;
}
else
{//unknown, ignore
Console.Error.WriteLine(string.Format("Unknown, name={0}, i={1}, genotype={2} {3} {4}", locus.MarkerId, i, parts[i], parts[i + 1], parts[i + 2]));
}
}
locus.Allele1Frequency = ((double)(count2)) / (count1 + count2);
}
}
PlinkLocus.WriteToFile(_options.OutputFile, locusList, false, true);
return(new string[] { _options.OutputFile });
}
