README.md

In CathyCha/BubbleGSEA: Bubble Graph for disease phenotyp enrichment results

BubbleEnrich

 

Yeon Joo Cha

1. Description:
2. Installations
3. Overview
4. Contributions
5. Quick Demo
6. Acknowledgement

Description

This package creates a bubble graph of disease phenotypes from a gene enrichment analysis done on a gene set of interest.

 

Installation

require("devtools")
install_github("CathyCha/BubbleEnrich")
library("BubbleEnrich")

Overview

Quick visualization of what the idea of the visualization of the package is:

 

The package tree structure is provided below.

 --BubbleEnrich/
   |__.gitignore
   |__.Rbuildignore
   |__.Rhistory
   |__BubbleEnrich.Rproj
   |__data/
      |__disgeneAnnot.rda
      |__HGNCAnnot.rda
   |__DESCRIPTION
   |__inst/
      |__CITATION
      |__extdata/
         |__CHA_Y_A1.png
         |__Rplot.png
         |__shiny.png
      |__shiny-scripts/
         |__app.R
   |__LICENSE
   |__LICENSE.md
   |__man/
      |__BubbleEnrich.Rd
      |__BubbleEnrichShiny.Rd
      |__disgeneAnnot.Rd
      |__geneIDsort.Rd
      |__HGNCAnnot.Rd
      |__userInput.Rd
   |__NAMESPACE
   |__R/
      |__BubbleEnrich.R
      |__BubbleEnrichShiny.R
      |__colourInput.R
      |__data.R
      |__geneIDsort.R
      |__sysdata.rda
      |__userInput.R
   |__README.md
   |__tests/
      |__testthat.R
      |__testthat/
         |__test-BubbleEnrich.R
   |__vignettes/
      |__.gitignore
      |__IntroductionBubbleEnrich.Rmd

 

Contributions

The author of this package is Yeon Joo (Cathy) Cha. The function available in this package is:

library(BubbleEnrich)
lsf.str("package:BubbleEnrich")

• BubbleEnrich
• BubbleEnrichShiny
• colourInput
• geneIDsort
• userInput

The function BubbleEnrich was authored by Yeon Joo Cha and makes use of the enricher() function from clusterProfiler package along with disease to gene annotations from DisGeNET to get disease phenotype enrichment results of the gene set of interest and HGNC gene id to HGNC symbol annotation. It also makes use of the ggplot function and the ggrepel package to plot a bubble graph of the enrichment results.

 

The function BubbleEnrichShiny is a function to run the shiny app and was taken from BCB410 lecture notes taught by Anjali Silva at UofT.

 

The function geneIDsort was authored by Yeon Joo Cha and uses the HGNC gene id to HGNC symbol annotation data to map geneids in the enrichment result and replaces them with more reader friendly HGNC symbols.

 

The functions colourInput and userInput are authored by Yeon Joo Cha and are helper functions for the BubbleEnrich shiny application.

 

Quick Demo

About the data

The example data being used for demo

For gene set enrichment analysis, we need a ranked list of genes. DOSE provides an example dataset geneList which was derived from R package breastCancerMAINZ that contained 200 samples, including 29 samples in grade I, 136 samples in grade II and 35 samples in grade III.

 

Visualizations

Running the demo with the example data as default opens a shiny application...

BubbleEnrichShiny()

... with the following default visualization

DisGeNET for gene-disease annotations

Using the disease to gene annotations from DisGeNET

*Stored in ~/BubbleEnrich/data/disgeneAnnot.rda

http://www.disgenet.org/static/disgenet_ap1/files/downloads/all_gene_disease_associations.tsv.gz

> head(disgeneAnnot)
  diseaseId geneId                   diseaseName
1  C0019209      1                  Hepatomegaly
2  C0013080      1                 Down Syndrome
3  C0036341      1                 Schizophrenia
4  C0001418      1                Adenocarcinoma
5  C0002736      1 Amyotrophic Lateral Sclerosis
6  C0017636      1                  Glioblastoma

 

HGNC for geneID to HGNC symbol annotations

Using the HGNC annotation data to map geneIDs from clusterProfiler to more reader friendly HGNC symbols.

https://www.genenames.org/cgi-bin/download/custom?col=gd_hgnc_id&col=gd_app_sym&col=gd_app_name&col=gd_status&col=gd_prev_sym&col=gd_aliases&col=gd_pub_chrom_map&col=gd_pub_acc_ids&col=gd_pub_refseq_ids&col=md_eg_id&status=Approved&status=Entry%20Withdrawn&hgnc_dbtag=on&order_by=gd_app_sym_sort&format=text&submit=submit

> head(HGNCAnnot)
  HGNC.ID Approved.symbol
1       5            A1BG
2   37133        A1BG-AS1
3   24086            A1CF
4       6           A1S9T
5       7             A2M
6   27057         A2M-AS1

Using your own data

If you are using your own gene set, it should be numeric csv file.

Acknowledgement

Enrichment functions from the clusterProfiler package in bioconductor was used to perform the enrichment analysis and output a enriched set result for the plotting of the bubble graph.

Acknowledgment to the DOSE package to for providing the example dataset for the demo of this package.

Thank you to Professor Boris Steipe for providing a R package template, rpt (https://github.com/hyginn/rpt), for BCB coursework.

 

 

CathyCha/BubbleGSEA documentation built on Dec. 8, 2019, 7:39 a.m.