getNEMO: Get subtypes from NEMO

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

Description

This function wraps the NEMO (Neighborhood based multi-omics clustering) algorithm and provides standard output for 'getMoHeatmap()' and 'getConsensusMOIC()'.

Usage

getNEMO(
  data = NULL,
  N.clust = NULL,
  type = rep("gaussian", length(data)),
  num.neighbors = NA
)

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.
num.neighbors	The number of neighbors to use for each omic.

Value

A list with the following components:

fit an object returned by nemo.clustering.

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

Rappoport N, Shamir R (2019). NEMO: cancer subtyping by integration of partial multi-omic data. Bioinformatics, 35(18):3348-3356.

Examples

# There is no example and please refer to vignette.

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