Non-negative matrix factorization (NMF) of a matrix containing SNP probe signals.
fitSnpNmf(V, acc=0.02, maxIter=10, maxIterRlm=20, refs=NULL)Returns a list:
The Kx2 matrix containing allele-specific affinity estimates.
A 2xI matrix containing allele-specific copy number estimates.
TRUE if the algorithm converged, otherwise FALSE.
If not applicable, it is NA.
The number of iteration ran before stopping.
If not applicable, it is NA.
An KxI matrix where I is the number of arrays and K is the
number of probe where K should be even (K=2L).
A positive double specifying the converence threshold. For
more details on convergence, see below.
A positive integer specifying the maximum number of
iterations used to calculate the decomposition.
A positive integer specifying the maximum number of
iterations used in rlm.
An index vector (integer or logical) specifying the
reference samples. If NULL, all samples are used as a reference.
The algorithm is considered to have converged when the maximum update
of any allele-specific copy number of any array (H) is greater
than acc.
WHInit(), robustWInit(), robustHInit(), and
removeOutliers().