canopy.cluster {Canopy} | R Documentation |
EM algorithm for multivariate clustering of SNAs.
canopy.cluster(R, X, num_cluster, num_run, Mu.init = NULL, Tau_Kplus1 = NULL)
R |
alternative allele read depth matrix |
X |
total read depth matrix |
num_cluster |
number of mutation clusters (BIC as model selection metric) |
num_run |
number of EM runs for estimation for each specific number of clusters (to avoid EM being stuck in local optima) |
Mu.init |
(optional) initial value of the VAF centroid for each mutation cluster in each sample |
Tau_Kplus1 |
(optional) pre-specified proportion of noise component in clustering, uniformly distributed between 0 and 1 |
Matrix of posterior probability of cluster assignment for each mutation.
Yuchao Jiang yuchaoj@wharton.upenn.edu
data(AML43)
R = AML43$R
X = AML43$X
Mu = AML43$Mu
Tau = AML43$Tau
pG = canopy.cluster.Estep(Tau, Mu, R, X)