/// <summary>
/// Factory method for implementations of this interface
/// </summary>
/// <returns>The expression data.</returns>
/// <param name="filename">Filename.</param>
/// <param name="rnaType">Rna type.</param>
/// <param name="filetype">Filetype.</param>
/// <param name="annotation">Annotation.</param>
public static IExpressionData LoadExpressionData(string filename, string rnaType, string filetype, IAnnotation annotation)
{
Console.WriteLine("\tLoading expression file " + filename + " ... ");
IExpressionData data = null;
if (filetype == "gtf" || filetype == ".gtf")
{
data = IUnknown.QueryInterface <IExpressionData>(new GtfExpressionFile(GtfExpressionFile.ExpressionTypeFromString(rnaType), filename, annotation));
}
else
{
data = IUnknown.QueryInterface <IExpressionData>(new BedExpressionFile(filename, BedFile.BedExpression, annotation));
}
Console.WriteLine("\ttranscript count: " + data.Transcripts.Count);
Console.WriteLine("\tgene count: " + data.Genes.Count);
return(data);
}
/// <summary>
/// Gets the link lengths orientated by TSS strand
/// </summary>
/// <returns>The link lengths.</returns>
/// <param name="expressionData">Expression data.</param>
public List <int> DirectionalLinkLengths(IExpressionData expressionData)
{
return(this.Links.Select(x => expressionData.Transcripts.ContainsKey(x.TranscriptName) ?
(expressionData.Transcripts[x.TranscriptName].Strand == "+" ?
x.LinkLength : -x.LinkLength) : x.LinkLength).ToList());
}
