module_NMF: module_NMF

Description Usage Arguments Value Author(s) References Examples

View source: R/miRSM.R

Description

Identification of gene modules from matched ceRNA and mRNA expression data using NMF package

Usage

1
2
3
4
5
6
7
8
module_NMF(
  ceRExp,
  mRExp,
  NMF.algorithm = "brunet",
  num.modules = 10,
  num.ModuleceRs = 2,
  num.ModulemRs = 2
)

Arguments

ceRExp

A SummarizedExperiment object. ceRNA expression data: rows are samples and columns are ceRNAs.

mRExp

A SummarizedExperiment object. mRNA expression data: rows are samples and columns are mRNAs.

NMF.algorithm

Specification of the NMF algorithm, including 'brunet' (default), 'Frobenius', 'KL', 'lee', 'nsNMF', 'offset', 'siNMF', 'snmf/l', 'snmf/r'.

num.modules

The number of modules to be identified.

num.ModuleceRs

The minimum number of ceRNAs in each module.

num.ModulemRs

The minimum number of mRNAs in each module.

Value

GeneSetCollection object: a list of module genes.

Author(s)

Junpeng Zhang (https://www.researchgate.net/profile/Junpeng_Zhang3)

References

Gaujoux R, Seoighe C. A flexible R package for nonnegative matrix factorization. BMC Bioinformatics. 2010, 11:367.

Examples

1
2
3
4
5
data(BRCASampleData)
# Reimport NMF package to avoid conflicts with DelayedArray package
library(NMF)
modulegenes_NMF <- module_NMF(ceRExp[, seq_len(10)],
    mRExp[, seq_len(10)])

zhangjunpeng411/miRSM documentation built on Nov. 28, 2020, 7 a.m.