runSNF: Run SNF method to get the subtyping results.

In GaoLabXDU/CEPICS: CEPICS: a comparison and evaluation platform for integration methods in cancer subtyping

Description

Using SNFTool R package to get the subtyping results.

Usage

runSNF(Wall, k = NULL, t = 20, kMax = 5)

Arguments

Wall	A list of different omics data. Each data in data list should be format as a data matrix with rows representing features and columns representing samples.
k	An integer number means the number of neighbors in K-nearest neighbors.Default NULL.
t	An integer number means the number of iterations for the diffusion process. Default 20.
kMax	An integer value means the maximize number of clusters we will try. Default 5.

Value

The sample clustering results matrix including 2 to kMax clustering results, and sample similarity matrix.

References

Wang,B. et al. (2014) Similarity network fusion for aggregating data types on a genomic scale. Nature Methods, 11, 333-337.

Concise description can be found here: http://compbio.cs.toronto.edu/SNF/SNF/Software.html

Examples

data(COAD_Methy, COAD_miRNA, COAD_mRNA)
datalist <- list(COAD_Methy, COAD_miRNA, COAD_mRNA)
res <- runSNF(datalist, k = 10, t = 20, kMax = 5)

GaoLabXDU/CEPICS documentation built on June 9, 2020, 2:31 a.m.