enrichmentMap: enrichmentMap

In aiminy/PathwaySplice: An R Package for Adjusting Bias in Gene Set Enrichment Analysis

Description

enrichmentMap is used to draw network based on similarities between GOs

Usage

enrichmentMap(GoSeqRes, gene.set.type = "GO", n = 50, fixed = TRUE,
  vertex.label.font = 1, SimilarityThreshold, ...)

Arguments

GoSeqRes	object returned from Run_pathwaysplice
gene.set.type	whether you are interested in GO, KEGG, or other pathways
n	maximum number of category to shown
fixed	if set to FALSE, will invoke tkplot
vertex.label.font	font size of vertex label
SimilarityThreshold	threshold for defining similarity between GOs
...	additional parameter

Value

A figure for visualizing network

Author(s)

Aimin created this funciton based on enrichMap function in G Yu's DOSE R package

Examples

data(mds)

Example.Go.adjusted.by.exon<-Run_pathwaysplice(mds,ad="exon_SJ",
sub_feature="E",0.05,genomeID="hg19",geneID="ensGene",
gene_model=hg19,method="Wallenius")

re.w.adjusted<-enrichmentMap(Example.Go.adjusted.by.exon,n=5,SimilarityThreshold=0)

aiminy/PathwaySplice documentation built on May 10, 2019, 7:38 a.m.