module_FA: module_FA

Description Usage Arguments Value Author(s) References Examples

View source: R/miRSM.R

Description

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

Usage

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module_FA(
  Modulelist,
  GOont = "BP",
  Diseaseont = "DO",
  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.

Diseaseont

One of 'DO', and 'DOLite' 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_Zhang3)

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.

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

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## 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 Nov. 28, 2020, 7 a.m.