getPINSPlus: Get subtypes from PINSPlus

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

Description

This function wraps the PINSPlus (Perturbation Clustering for data INtegration and disease Subtyping) algorithm and provides standard output for 'getMoHeatmap()' and 'getConsensusMOIC()'.

Usage

getPINSPlus(
  data = NULL,
  N.clust = NULL,
  type = rep("gaussian", length(data)),
  norMethod = "none",
  clusteringMethod = "kmeans",
  iterMin = 50,
  iterMax = 500
)

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.
norMethod	A string vector indicate the normalization method for consensus clustering.
clusteringMethod	The name of built-in clustering algorithm that PerturbationClustering will use. Currently supported algorithm are kmeans, pam and hclust. Default value is "kmeans".
iterMin	The minimum number of iterations. Default value is 50
iterMax	The maximum number of iterations. Default value is 500.

Value

A list with the following components:

fit an object returned by PerturbationClustering.

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

Nguyen H, Shrestha S, Draghici S, Nguyen T (2019). PINSPlus: a tool for tumor subtype discovery in integrated genomic data. Bioinformatics, 35(16):2843-2846.

Examples

# There is no example and please refer to vignette.

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