module_igraph: module_igraph

In zhangjunpeng411/miRSM: Inferring miRNA sponge modules in heterogeneous data

module_igraph

Description

Identification of gene modules from matched ceRNA and mRNA expression data or single gene expression data using igraph package

Usage

module_igraph(
  ceRExp,
  mRExp = NULL,
  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	NULL (default) or 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-Zhang-2)

References

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

Examples

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

zhangjunpeng411/miRSM documentation built on Sept. 23, 2024, 4:37 a.m.