SIMLR Estimate Number of Clusters — SIMLR_Estimate_Number_of

estimate the number of clusters by means of two huristics as discussed in the SIMLR paper

SIMLR_Estimate_Number_of_Clusters(X, NUMC = 2:5, cores.ratio = 1)

Arguments

X: an (m x n) data matrix of gene expression measurements of individual cells
NUMC: vector of number of clusters to be considered
cores.ratio: ratio of the number of cores to be used when computing the multi-kernel

Value

a list of 2 elements: K1 and K2 with an estimation of the best clusters (the lower values the better) as discussed in the original paper of SIMLR

Examples

data(BuettnerFlorian)
SIMLR_Estimate_Number_of_Clusters(BuettnerFlorian$in_X,
   NUMC = 2:5,
   cores.ratio = 0)
#> $K1
#> [1] -63.04223 -19.49278 -23.77182  13.30109
#> 
#> $K2
#> [1] -94.56335 -25.99037 -29.71477  15.96130
#>