SIMLR {SIMLR}R Documentation

SIMLR

Description

perform the SIMLR clustering algorithm

Usage

SIMLR(X, c, no.dim = NA, k = 10, if.impute = FALSE,
  normalize = FALSE, cores.ratio = 1)

Arguments

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

Value

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

Examples

SIMLR(X = BuettnerFlorian$in_X, c = BuettnerFlorian$n_clust, cores.ratio = 0)


[Package SIMLR version 1.10.0 Index]