/**
* Computes the euclidean centroid, it may not be the formal centroid for different metrics but
* intuitively the average counts should provide a good cluster representative which is what this
* method intends to return
*
* @param pwmSet - Collection of pwms from which to compute the centroid0
* @return The euclidean centroid
* @throws IllegalArgumentException - When not all PWMs have the same dimension.
*/
public PositionWeightMatrix centroidOf(Collection<PositionWeightMatrix> pwmSet)
throws IllegalArgumentException {
Matrix centroidMatrix = null;
Iterator<PositionWeightMatrix> pwmIt = pwmSet.iterator();
if (pwmIt.hasNext()) {
PositionWeightMatrix first = pwmIt.next();
PositionWeightColumn firstCol = first.get(0);
centroidMatrix = new Matrix(firstCol.getAlphabetSize(), first.getNumCol());
addToCentroid(centroidMatrix, first);
}
while (pwmIt.hasNext()) {
PositionWeightMatrix pwm = pwmIt.next();
if (pwm.getNumCol() != centroidMatrix.getColumnDimension()) {
throw new IllegalArgumentException(
"Error computing centroid. All PWMs in set should have the same dimension");
}
addToCentroid(centroidMatrix, pwm);
}
centroidMatrix.times(1 / (double) pwmSet.size());
PositionWeightMatrix centroid = new PositionWeightMatrix("centroid");
for (int j = 0; j < centroidMatrix.getColumnDimension(); j++) {
centroid.addColumn(centroidMatrix.getColumn(j));
}
return centroid;
}
/**
* Creates a PWM of similar dimension to this PWM but with all columns set to the given vector,
* usually a neutral mutation vector.
*
* @param column
* @return
*/
public PositionWeightMatrix createIsoPWM(double[] column, String name) {
PositionWeightMatrix pwm = new PositionWeightMatrix(name);
for (int i = 0; i < size(); i++) {
pwm.addColumn(column);
}
return pwm;
}
public void addPWMColumn(double[] col) {
pwm.addColumn(col);
}