GOEnrich: GO enrichment analysis

In zexllin/lncRNAtools: Do lncRNA bioinformatics Advanced analysis,includes routine analysis of mRNA/miRNA

Description

Performs Gene Ontology (GO) enrichment analyses by clusterProfiler packages

Usage

GOEnrich(gene, simplify = TRUE, level = 0, data.type = "")

Arguments

gene	a vector of Ensembl gene id
simplify	logical, specifying whether to remove redundant GO terms. Default simplify=TRUE
level	a numeric value, restrict the GO enrichment result at a specific GO level. Default is 0, which means all terms should be returned
data.type	prefix for Save file names

Value

return a data frame of GO enrichment analysis result, and write it to file

Author(s)

zexl

References

Yu G, Wang LG, Han Y, He QY. clusterProfiler: an R package for comparing biological themes among gene clusters. Omics: a journal of integrative biology. 2012 May 1;16(5):284-7.

Yu G, Wang LG, Yan GR, He QY. DOSE: an R/Bioconductor package for disease ontology semantic and enrichment analysis. Bioinformatics. 2014 Oct 17;31(4):608-9.

Examples

    Upgene<-deall[which(deall$logFC>=1),]
    UpgeneGoOut<-GOEnrich(
            gene = rownames(Upgene),
            data.type = 'RNA_Up'
            )

zexllin/lncRNAtools documentation built on Jan. 1, 2021, 1:52 p.m.