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 ITCGATechnology GetTechnology(this TCGATechnologyType ttype)
{
switch (ttype)
{
case TCGATechnologyType.Affy:
case TCGATechnologyType.Agilent:
return(TCGATechnology.Microarray);
case TCGATechnologyType.RPKM:
return(TCGATechnology.RNAseq_RPKM);
case TCGATechnologyType.RSEM:
return(TCGATechnology.RNAseq_RSEM);
default:
throw new Exception("Unknown type " + ttype);
}
}
public static bool HasSample(this Dictionary <TCGATechnologyType, Dictionary <TCGASampleType, List <BarInfo> > > tumormap, TCGATechnologyType tType)
{
return(tumormap[tType].GetSampleCount() > 0);
}
private static void AddDataset(Dictionary <TCGATechnologyType, Dictionary <TCGASampleType, List <BarInfo> > > tumormap, TCGATechnologyType technolyType, DatasetInfo datasetInfo)
{
var map = new Dictionary <TCGASampleType, List <BarInfo> >();
tumormap[technolyType] = map;
foreach (var type in EnumUtils.EnumToArray <TCGASampleType>())
{
map[type] = new List <BarInfo>();
}
if (datasetInfo == null)
{
return;
}
foreach (var key in datasetInfo.BarInfoListMap)
{
var type = TCGAUtils.GetSampleType(key.Key);
map[type].Add(key.Value.First());
}
}
