module_igraph {miRSM} | R Documentation |
Identification of gene modules from matched ceRNA and mRNA expression data using igraph package
module_igraph( ceRExp, mRExp, cor.method = "pearson", pos.p.value.cutoff = 0.01, cluster.method = "greedy", num.ModuleceRs = 2, num.ModulemRs = 2 )
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. |
GeneSetCollection object: a list of module genes.
Junpeng Zhang (https://www.researchgate.net/profile/Junpeng_Zhang3)
Csardi G, Nepusz T. The igraph software package for complex network research, InterJournal, Complex Systems. 2006:1695.
data(BRCASampleData) modulegenes_igraph <- module_igraph(ceRExp[, seq_len(10)], mRExp[, seq_len(10)])