SIMLR {SIMLR} | R Documentation |
perform the SIMLR clustering algorithm
SIMLR( X, c, no.dim = NA, k = 10, if.impute = FALSE, normalize = FALSE, cores.ratio = 1 )
X |
an (m x n) data matrix of gene expression measurements of individual cells or and object of class SCESet |
c |
number of clusters to be estimated over X |
no.dim |
number of dimensions |
k |
tuning parameter |
if.impute |
should I traspose the input data? |
normalize |
should I normalize the input data? |
cores.ratio |
ratio of the number of cores to be used when computing the multi-kernel |
clusters the cells based on SIMLR and their similarities
list of 8 elements describing the clusters obtained by SIMLR, of which y are the resulting clusters: y = results of k-means clusterings, S = similarities computed by SIMLR, F = results from network diffiusion, ydata = data referring the the results by k-means, alphaK = clustering coefficients, execution.time = execution time of the present run, converge = iterative convergence values by T-SNE, LF = parameters of the clustering
data(BuettnerFlorian) SIMLR(X = BuettnerFlorian$in_X, c = BuettnerFlorian$n_clust, cores.ratio = 0)