This function works on a Vmat (the output of computeVmat()). It shuffles the matrix to randomize the fragment densities.
shuffleVmat(Vmat)
A Vmat, usually output of computeVmat
A shuffled Vmat object
data(bam_test)
data(ce11_all_REs)
Vmat <- computeVmat(bam_test, ce11_all_REs)
Vmat <- shuffleVmat(Vmat)