smfishHmrf.generate.centroid {smfishHmrf} | R Documentation |
Generate cluster centroids, where input is given as a matrix.
Description
This function assumes that the input gene expression matrix file has been already loaded into a matrix. The function accepts a matrix and applies kmeans clustering to generate cluster centroids.
Usage
smfishHmrf.generate.centroid(y, par_k, par_seed = -1, nstart)
Arguments
y |
expression matrix |
par_k |
number of clusters |
par_seed |
random generator seed (to fix it set it to above 0, or -1 if no fixing). Change the par_seed to vary the initialization. |
nstart |
number of starts (kmeans parameter). It is recommended to set nstart to at least 100 (preferrably 1000). |
Value
A kmeans list with centers and cluster fields
Examples
data(seqfishplus)
kk<-smfishHmrf.generate.centroid(seqfishplus$y, par_k=9, par_seed=100, nstart=100)
[Package smfishHmrf version 0.1 Index]