Pathway Enrichment Analysis • Linkage

Linkage can help you visualize tabular and graphical pathway enrichment results of interested gene lists. The GOEnrichment() and KEGGEnrichment() functions allow you to input a list of interested genes and set four key parameters (i.e., adjusted pvalue cutoff, qvalue cutoff, minimal size of annotated genes for testing, and maximal size of annotated genes for testing) for GO or KEGG pathway enrichment analysis.

library(Linkage)
data("SASPGeneSet")
go <-
  GOEnrichment(gene_list = SASPGeneSet,
               Species = "Homo",
               genelist_idtype = "external_gene_name")
KEGG <-
  KEGGEnrichment(
    gene_list = SASPGeneSet,
    Species = "Homo",
    genelist_idtype = "external_gene_name"
  )

Linkage offers several types of visual charts to interpret the functional results from multiple perspectives.

EnrichDotPlot(go)

EnrichBarPlot(go)

EnrichUpsetPlot(go)

EnrichCnetPlot(go)

EnrichWordCloud(go, Type = "GO")