module_FA: module_FA

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

module_FA

Description

Functional analysis of miRNA sponge modules, including functional enrichment and disease enrichment analysis

Usage

module_FA(
  Modulelist,
  GOont = "BP",
  KEGGorganism = "hsa",
  Reactomeorganism = "human",
  OrgDb = "org.Hs.eg.db",
  padjustvaluecutoff = 0.05,
  padjustedmethod = "BH",
  Analysis.type = c("FEA", "DEA")
)

Arguments

Modulelist	List object: a list of miRNA sponge modules.
GOont	One of 'MF', 'BP', and 'CC' subontologies.
KEGGorganism	Organism, supported organism listed in http://www.genome.jp/kegg/catalog/org_list.html.
Reactomeorganism	Organism, one of 'human', 'rat', ' mouse', 'celegans', 'yeast', 'zebrafish', 'fly'.
OrgDb	OrgDb
padjustvaluecutoff	A cutoff value of adjusted p-values.
padjustedmethod	Adjusted method of p-values, can select one of 'holm', 'hochberg', 'hommel', 'bonferroni', 'BH', 'BY', 'fdr', 'none'.
Analysis.type	The type of functional analysis selected, including 'FEA' (functional enrichment analysis) and 'DEA' (disease enrichment analysis).

Value

List object: a list of enrichment analysis results.

Author(s)

Junpeng Zhang (https://www.researchgate.net/profile/Junpeng-Zhang-2)

References

Zhang J, Liu L, Xu T, Xie Y, Zhao C, Li J, Le TD (2019). “miRspongeR: an R/Bioconductor package for the identification and analysis of miRNA sponge interaction networks and modules.” BMC Bioinformatics, 20, 235.

Zhang J, Liu L, Zhang W, Li X, Zhao C, Li S, Li J, Le TD. miRspongeR 2.0: an enhanced R package for exploring miRNA sponge regulation. Bioinform Adv. 2022 Sep 2;2(1):vbac063.

Yu G, Wang L, Han Y, He Q (2012). “clusterProfiler: an R package for comparing biological themes among gene clusters.” OMICS: A Journal of Integrative Biology, 16(5), 284-287.

Examples

## Not run: 
data(BRCASampleData)
modulegenes_WGCNA <- module_WGCNA(ceRExp, mRExp)
# Identify miRNA sponge modules using sensitivity RV coefficient (SRVC)
miRSM_WGCNA_SRVC <- miRSM(miRExp, ceRExp, mRExp, miRTarget,
                        modulegenes_WGCNA, method = "SRVC",
                        SMC.cutoff = 0.01, RV_method = "RV")
miRSM_WGCNA_SRVC_genes <- miRSM_WGCNA_SRVC[[2]]
miRSM_WGCNA_SRVC_FEA <- module_FA(miRSM_WGCNA_SRVC_genes, Analysis.type = 'FEA')
miRSM_WGCNA_SRVC_DEA <- module_FA(miRSM_WGCNA_SRVC_genes, Analysis.type = 'DEA')

## End(Not run)

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