SIMLR_Large_Scale {SIMLR}R Documentation

SIMLR Large Scale

Description

perform the SIMLR clustering algorithm for large scale datasets

Usage

SIMLR_Large_Scale(X, c, k = 10, kk = 100, if.impute = FALSE, normalize = FALSE)

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

k

tuning parameter

kk

number of principal components to be assessed in the PCA

if.impute

should I traspose the input data?

normalize

should I normalize the input data?

Value

clusters the cells based on SIMLR Large Scale 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, S0 = similarities computed by SIMLR, F = results from the large scale iterative procedure, ydata = data referring the the results by k-means, alphaK = clustering coefficients, val = distances from the k-nearest neighbour search, ind = indeces from the k-nearest neighbour search, execution.time = execution time of the present run

Examples

data(ZeiselAmit)
resized = ZeiselAmit$in_X[, 1:340]
## Not run: 
SIMLR_Large_Scale(X = resized, c = ZeiselAmit$n_clust, k = 5, kk = 5)

## End(Not run)


[Package SIMLR version 1.19.1 Index]