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 1.13.1 Index]