mnemk {mnem} | R Documentation |
High level function for learning the number of components k, if unknown.
mnemk( D, ks = seq_len(5), man = FALSE, degree = 4, logtype = 2, pen = 2, useF = FALSE, Fnorm = FALSE, ... )
D |
data with cells indexing the columns and features (E-genes) indexing the rows |
ks |
vector of number of components k to test |
man |
logical. manual data penalty, e.g. man=TRUE and pen=2 for an approximation of the Akaike Information Criterion |
degree |
different degree of penalty for complexity: positive entries of transitively reduced phis or phi^r (degree=0), phi^r and mixture components minus one k-1 (1), phi^r, k-1 and positive entries of thetas (2), positive entries of transitively closed phis or phi^t, k-1 (3), phi^t, theta, k-1 (4, default), all entries of phis, thetas and k-1 (5) |
logtype |
logarithm type of the data (e.g. 2 for log2 data or exp(1) for natural) |
pen |
penalty weight for the data (e.g. pen=2 for approximate Akaike Information Criterion) |
useF |
use F (see publication) as complexity instead of phi and theta |
Fnorm |
normalize complexity of F, i.e. if two components have the same entry in F, it is only counted once |
... |
additional parameters for the mnem main function |
list containing the result of the best k as an mnem object and the raw and penalized log likelihoods
Martin Pirkl
sim <- simData(Sgenes = 3, Egenes = 2, Nems = 2, mw = c(0.4,0.6)) data <- (sim$data - 0.5)/0.5 data <- data + rnorm(length(data), 0, 1) result <- mnemk(data, ks = seq_len(2), starts = 1)