getSNF: Get subtypes from SNF

In xlucpu/MOVICS: Multi-Omics integration and VIsualization in Cancer Subtyping

Description

This function wraps the SNF (Similarity Network Fusion) algorithm and provides standard output for 'getMoHeatmap()' and 'getConsensusMOIC()'.

Usage

getSNF(
  data = NULL,
  N.clust = NULL,
  type = rep("gaussian", length(data)),
  K = 30,
  t = 20,
  sigma = 0.5
)

Arguments

data	List of matrices.
N.clust	Number of clusters.
type	Data type corresponding to the list of matrics, which can be gaussian, binomial or possion.
K	An integer value to indicate the number of neighbors in K-nearest neighbors part of the algorithm.
t	An integer value to indicate the number of interations for the diffusion process.
sigma	A numerical value to indicate the variance for local model.

Value

A list with the following components:

fit an object returned by SNF.

clust.res a data.frame storing sample ID and corresponding clusters.

mo.method a string value indicating the method used for multi-omics integrative clustering.

References

Wang B, Mezlini AM, Demir F, et al (2014). Similarity network fusion for aggregating data types on a genomic scale. Nat Methods, 11(3):333-337.

Examples

# There is no example and please refer to vignette.

xlucpu/MOVICS documentation built on July 24, 2021, 9:23 p.m.