Set up operations with freeCount | R bloggers

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Overview

In general, set operations are very useful for comparing lists of things. These lists can contain all possible strings, such as gene or species names.

Set operations are also a good way to identify unique or shared genes in sets of analysis results. The free phone The SO app helps you perform fixed operations with gene lists, which can be produced based on differential expression or network analysis.

Potential questions

What shared genes drive the patterns of DE across genotypes?

Which genes drive the patterns of DE across treatments?

Which DE genes share coexpression patterns in a given network module?

Learning objectives

Learn how to perform set operations with ggVennDiagram
Practice comparing lists of gene names
Understand how to identify shared and unique genes

This tutorial is the fifth in a series on omics data analysis:

Differential expression analysis with freeCount
Functional analysis with freeCount
Network analysis with freeCount
Functional analysis of networks with freeCount

ggVennDiagram

The ggVennDiagram The R package enables nice Venn plots with 2-7 sets and generates publication quality figures. It also supports perturbed plots with unlimited sets as of version 1.4.4.

Before you start

The exercise in this tutorial uses the freeCount apps in RStudio on a PC. Make sure you have downloaded, installed, and installed the following tools up to date on your PC:

R software environment
RStudio desktop application

For Windows usersadditionally install RTools.

It is also possible to run the freeCount apps online via Posit Cloud. To see how, check out the freeCount Bioinformatics analysis apps on Posit Cloud self-study.

Input data

Download the tribolium gene list 1 file
Download the tribolium gene list 2 file
Download the tribolium gene list 3 file
Download the tribolium gene list 4 file

Tip! After clicking on the data linked above, right click and select Save as… to download the above files in the necessary formats.

The Analysis App

The following steps show you how to download and launch the freeCount set operations (SO) app.

Download the free Count R Shiny applications
1. Go to https://github.com/ElizabethBrooks/freeCount
2. Click on the green < > Code knob
3. Click Download ZIP
Grab the freeCount-main folder
Navigate to the apps folder
Open the SO.R file in RStudio
Click Install on the yellow banner to install the necessary R packages (or run the code on lines 10 through 15)
Click on the Run app button in the top right corner of the source panel

Analysis process

Complete the following steps to create a

Upload the four data sets
Download the two-way Venn diagram results
Download the results of the three-way Venn diagram
Download the results of the four-way Venn diagram

1. Upload data

Upload the datasets (lists) you want to compare.

Input data

First, upload a file with the list of things you want to compare. These lists can contain all kinds of strings, such as gene or species names. In this tutorial we will use the tribolium gene list 1 file.
Then upload the second file with a list. In this tutorial we will use the tribolium gene list 2 file. After the second file is uploaded, the analysis results will appear. You can also continue to upload sets/lists that you want to compare (maximum 4 sets).
Third, upload the third file with a list. In this tutorial we will use the tribolium gene list 3 file.
Finally, upload the fourth file with a list. In this tutorial we will use the tribolium gene list 4 file. The free Count SO app allows you to compare up to 4 sets.

Note that the gene names in these files are actually IDs specific to the species and database.

2. Download Two-Way Venn

Download the two-way Venn diagram results from the Venn diagrams tab.

Below each Venn diagram are dropdowns and download buttons, which allow you to export specific set intersections. This allows you to select unique or shared gene lists for the sets you are comparing.

Set up operations with freeCount | R bloggers