In llrs/GSEAdv: Analyze Gene Sets Collections Properites

knitr::opts_knit$set(root.dir = ".")
knitr::opts_chunk$set(collapse = TRUE, warning = TRUE)
BiocStyle::markdown()
library("BiocStyle")
library("GSEAdv")

Introduction

Bioconductor provides with the package r Biocpkg("GSEABase") which provides the basic methods and classes to join, create, and manipulate the gene sets. However few (if any) packages take into account the relationship between genes and gene sets when using them. This package builds upon GeneSetCollection providing methods to describe the relationship between genes and gene sets, evaluate the relationship between genes and gene sets, and simulate gene set collections.

Installation

You can install it from github to get the latest version:

devtools::install_github("llrs/GSEAdv")

or from Bioconductor for a stable release:

if (!requireNamespace("BiocManager", quietly = TRUE))
    install.packages("BiocManager")
BiocManager::install("BioCor", version = "3.8")

Semantics

Thorough the vignettes and the help page a group of genes is both referred as gene sets or as pathways. A pathway or a gene set is defined as a group of genes (more than one) which can't contain twice the same gene.

All the genes should use the same identifier type, Entrez, or a Symbol or Ensembl.

The function check returns a GeneSetCollection that complies with this principles:

fl <- system.file("extdata", "Broad.xml", package = "GSEABase")
gss <- getBroadSets(fl)
check(gss)

Usage

Once installed you just need to load it[^1]:

[^1]:To avoid a long message due to GSEAdv's dependencies it is recommend to use suppressPackageStartupMessages when loading this package.

library("GSEAdv")

The package is thought for three main cases, each one has its own vignette:

• r Biocpkg("GSEAdv", "vignette_describe.html", "*Description*")

To provide insight about the relationship between genes and gene sets.

• r Biocpkg("GSEAdv", "vignette_evaluate.html", "*Evaluation*")

Compare and estimate the relationship between genes and gene sets.

• r Biocpkg("GSEAdv", "vignette_simulate.html", "*Simulate*")

Given some approximations of the relationships between genes and gene sets creates a new gene set collection.

llrs/GSEAdv documentation built on May 29, 2019, 6 p.m.