getKeggDiagram: Display the enriched KEGG diagram of the KEGG pathway. This...

In NoRCE: NoRCE: Noncoding RNA Sets Cis Annotation and Enrichment

Description

Display the enriched KEGG diagram of the KEGG pathway. This function is specific to only one KEGG pathway id and identifies the enriched genes in the diagram.

Usage

getKeggDiagram(
  mrnaObject,
  pathway,
  org_assembly = c("hg19", "hg38", "mm10", "dre10", "rn6", "dm6", "ce11", "sc3")
)

Arguments

mrnaObject	Output of enrichment results
pathway	Kegg pathway term such as 'hsa04010'
org_assembly	Genome assembly of interest for the analysis. Possible assemblies are "mm10" for mouse, "dre10" for zebrafish, "rn6" for rat, "dm6" for fruit fly, "ce11" for worm, "sc3" for yeast, "hg19" and "hg38" for human

Value

Shows kegg diagram marked with an enriched genes in a browser

Examples

ncRNAPathway<-mirnaPathwayEnricher(gene = brain_mirna,
                                   org_assembly = 'hg19',near = TRUE)

getKeggDiagram(mrnaObject = ncRNAPathway, org_assembly ='hg19',
               pathway = ncRNAPathway@ID[1])

NoRCE documentation built on Nov. 8, 2020, 7:17 p.m.