clustNEM {mnem} | R Documentation |
This function clusters the data and performs standard nem on each cluster.
clustNEM( data, k = 2:10, cluster = NULL, starts = 1, logtype = 2, nem = TRUE, getprobspars = list(), getaffinitypars = list(), Rho = NULL, ... )
data |
data of log ratios with cells in columns and features in rows |
k |
number of clusters to check |
cluster |
given clustering has to correspond to the columns of data |
starts |
number of random starts for the kmeans algorithm |
logtype |
logarithm type of the data |
nem |
if FALSE only clusters the data |
getprobspars |
list of parameters for the getProbs function |
getaffinitypars |
list of parameters for the getAffinity function |
Rho |
perturbation matrix with dimensions nxl with n S-genes and l samples; either as probabilities with the sum of probabilities for a sample less or equal to 1 or discrete with 1s and 0s |
... |
additional arguments for standard nem function |
family of nems; the first k list entries hold full information of the standard nem search
comp |
list of all adjacency matrices phi |
mw |
vector of mixture weights |
probs |
fake cell probabilities (see mw: mixture weights) |
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) resulst <- clustNEM(data, k = 2:3)