/// <summary>
/// Constructs a design matrix for a FoldChangeDataSet.
/// If <paramref name="includeFeatureInteraction"/> is true, then the model is:
/// ABUNDANCE ~ FEATURE + SUBJECT + GROUP + FEATURE:GROUP
/// if false, then the model is:
/// ABUNDANCE ~ FEATURE + SUBJECT + GROUP
/// </summary>
/// <param name="dataSet"></param>
/// <param name="includeFeatureInteraction"></param>
/// <returns></returns>
public static DesignMatrix GetDesignMatrix(FoldChangeDataSet dataSet, bool includeFeatureInteraction)
{
var columnNames = new List <string>();
var matrixColumns = new List <double[]>();
var contrastValues = new List <double>();
columnNames.Add("Intercept");
matrixColumns.Add(Enumerable.Repeat(1.0, dataSet.RowCount).ToArray());
contrastValues.Add(0);
for (int iFeature = 1; iFeature < dataSet.FeatureCount; iFeature++)
{
columnNames.Add("Feature" + iFeature);
matrixColumns.Add(Enumerable.Range(0, dataSet.RowCount).Select(iRow => iFeature == dataSet.Features[iRow] ? 1.0 : 0.0).ToArray());
contrastValues.Add(0.0);
}
if (dataSet.RowCount != dataSet.SubjectCount)
{
int controlGroupCount = dataSet.SubjectControls.Count(f => f);
var subjectIndexes = Enumerable.Range(1, dataSet.SubjectCount - 1);
foreach (int iSubject in subjectIndexes)
{
columnNames.Add("Subject" + iSubject);
matrixColumns.Add(Enumerable.Range(0, dataSet.RowCount).Select(iRow => iSubject == dataSet.Subjects[iRow] ? 1.0 : 0.0).ToArray());
if (dataSet.IsSubjectInControlGroup(iSubject))
{
contrastValues.Add(-1.0 / controlGroupCount);
}
else
{
contrastValues.Add(1.0 / (dataSet.SubjectCount - controlGroupCount));
}
}
}
columnNames.Add("Control");
matrixColumns.Add(Enumerable.Range(0, dataSet.RowCount).Select(iRow => dataSet.IsRowInControlGroup(iRow) ? 1.0 : 0.0).ToArray());
contrastValues.Add(-1.0);
if (includeFeatureInteraction)
{
for (int iFeature = 1; iFeature < dataSet.FeatureCount; iFeature++)
{
columnNames.Add("Feature" + iFeature + "Interaction");
matrixColumns.Add(Enumerable.Range(0, dataSet.RowCount).Select(iRow =>
iFeature == dataSet.Features[iRow] && dataSet.IsRowInControlGroup(iRow) ? 1.0 : 0.0).ToArray());
contrastValues.Add(-1.0 / dataSet.FeatureCount);
}
}
return(new DesignMatrix(dataSet, matrixColumns.ToArray(), contrastValues.Select(value => new[] { value }).ToArray(), columnNames.ToArray()));
}
/// <summary>
/// Constructs a design matrix for a FoldChangeDataSet.
/// If <paramref name="includeFeatureInteraction"/> is true, then the model is:
/// ABUNDANCE ~ FEATURE + SUBJECT + GROUP + FEATURE:GROUP
/// if false, then the model is:
/// ABUNDANCE ~ FEATURE + SUBJECT + GROUP
/// </summary>
/// <param name="dataSet"></param>
/// <param name="includeFeatureInteraction"></param>
/// <returns></returns>
public static DesignMatrix GetDesignMatrix(FoldChangeDataSet dataSet, bool includeFeatureInteraction)
{
var columnNames = new List<string>();
var matrixColumns = new List<double[]>();
var contrastValues = new List<double>();
columnNames.Add("Intercept");
matrixColumns.Add(Enumerable.Repeat(1.0, dataSet.RowCount).ToArray());
contrastValues.Add(0);
for (int iFeature = 1; iFeature < dataSet.FeatureCount; iFeature++)
{
columnNames.Add("Feature" + iFeature);
matrixColumns.Add(Enumerable.Range(0, dataSet.RowCount).Select(iRow=>iFeature == dataSet.Features[iRow] ? 1.0 : 0.0).ToArray());
contrastValues.Add(0.0);
}
if (dataSet.RowCount != dataSet.SubjectCount)
{
int controlGroupCount = dataSet.SubjectControls.Count(f => f);
var subjectIndexes = Enumerable.Range(1, dataSet.SubjectCount - 1);
foreach (int iSubject in subjectIndexes)
{
columnNames.Add("Subject" + iSubject);
matrixColumns.Add(Enumerable.Range(0, dataSet.RowCount).Select(iRow=>iSubject == dataSet.Subjects[iRow] ? 1.0 : 0.0).ToArray());
if (dataSet.IsSubjectInControlGroup(iSubject))
{
contrastValues.Add(-1.0/controlGroupCount);
}
else
{
contrastValues.Add(1.0 / (dataSet.SubjectCount - controlGroupCount));
}
}
}
columnNames.Add("Control");
matrixColumns.Add(Enumerable.Range(0, dataSet.RowCount).Select(iRow => dataSet.IsRowInControlGroup(iRow) ? 1.0 : 0.0).ToArray());
contrastValues.Add(-1.0);
if (includeFeatureInteraction)
{
for (int iFeature = 1; iFeature < dataSet.FeatureCount; iFeature++)
{
columnNames.Add("Feature" + iFeature + "Interaction");
matrixColumns.Add(Enumerable.Range(0, dataSet.RowCount).Select(iRow =>
iFeature == dataSet.Features[iRow] && dataSet.IsRowInControlGroup(iRow) ? 1.0 : 0.0).ToArray());
contrastValues.Add(-1.0 / dataSet.FeatureCount);
}
}
return new DesignMatrix(dataSet, matrixColumns.ToArray(), contrastValues.Select(value => new[]{value}).ToArray(), columnNames.ToArray());
}
