module_igraph: module_igraph

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 igraph package

Usage

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module_igraph(
  ceRExp,
  mRExp,
  cor.method = "pearson",
  pos.p.value.cutoff = 0.01,
  cluster.method = "greedy",
  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.

cor.method

The method of calculating correlation selected, including 'pearson' (default), 'kendall', 'spearman'.

pos.p.value.cutoff

The significant p-value cutoff of positive correlation.

cluster.method

The clustering method selected in igraph package, including 'betweenness', 'greedy' (default), 'infomap', 'prop', 'eigen', 'louvain', 'walktrap'.

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

Csardi G, Nepusz T. The igraph software package for complex network research, InterJournal, Complex Systems. 2006:1695.

Examples

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data(BRCASampleData)
modulegenes_igraph <- module_igraph(ceRExp[, seq_len(10)],
    mRExp[, seq_len(10)])

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