module_FA {miRSM} | R Documentation |
Functional analysis of miRNA sponge modules, including functional enrichment and disease enrichment analysis
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") )
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). |
List object: a list of enrichment analysis results.
Junpeng Zhang (https://www.researchgate.net/profile/Junpeng_Zhang3)
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.
## 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)