public static ExpressionMatrix ReadMatrix(this TCGATechnologyType ttt, TCGADataType tdt, List<BarInfo> bis, List<string> genes)
{
double?[,] data = new double?[genes.Count, bis.Count];
for (int i = 0; i < bis.Count; i++)
{
var reader = ttt.GetTechnology().GetReader();
var fn = tdt == TCGADataType.Count ? ttt.GetTechnology().GetCountFilename(bis[i].FileName) : bis[i].FileName;
var dd = reader.ReadFromFile(fn).Values.ToDictionary(m => m.Name, m => m.Value);
for (int j = 0; j < genes.Count; j++)
{
if (dd.ContainsKey(genes[j]))
{
data[j, i] = dd[genes[j]];
}
else
{
data[j, i] = null;
}
}
}
ExpressionMatrix result = new ExpressionMatrix();
result.Values = data;
result.Rownames = genes.ToArray();
result.Colnames = bis.ConvertAll(m => m.BarCode).ToArray();
return result;
}
public static ExpressionMatrix ReadMatrix(this TCGATechnologyType ttt, TCGADataType tdt, List <BarInfo> bis, List <string> genes)
{
double?[,] data = new double?[genes.Count, bis.Count];
for (int i = 0; i < bis.Count; i++)
{
var reader = ttt.GetTechnology().GetReader();
var fn = tdt == TCGADataType.Count ? ttt.GetTechnology().GetCountFilename(bis[i].FileName) : bis[i].FileName;
var dd = reader.ReadFromFile(fn).Values.ToDictionary(m => m.Name, m => m.Value);
for (int j = 0; j < genes.Count; j++)
{
if (dd.ContainsKey(genes[j]))
{
data[j, i] = dd[genes[j]];
}
else
{
data[j, i] = null;
}
}
}
ExpressionMatrix result = new ExpressionMatrix();
result.Values = data;
result.Rownames = genes.ToArray();
result.Colnames = bis.ConvertAll(m => m.BarCode).ToArray();
return(result);
}
public virtual IFileReader<ExpressionData> GetReader(TCGADataType tdt)
{
if (tdt == TCGADataType.Normalized)
{
return GetReader();
}
else
{
return GetCountReader();
}
}
public static string GetSuffix(this TCGADataType dt)
{
if (dt == TCGADataType.Count)
{
return("_Count");
}
else
{
return("");
}
}
public virtual IFileReader <ExpressionData> GetReader(TCGADataType tdt)
{
if (tdt == TCGADataType.Normalized)
{
return(GetReader());
}
else
{
return(GetCountReader());
}
}
