fgsList: A list of Functional Gene Set (FGS) to be used to run the...

In marchionniLab/RTopper: This package is designed to perform Gene Set Analysis across multiple genomic platforms

A list of Functional Gene Set (FGS) to be used to run the examples in the RTopper package

Description

A list containing distinct types of FGS (i.e. Gene Ontology, KEGG pathways). Each FGS is type is a list of named chararacter vectors, one for each FGS, containing the gene identifiers. Vectors names describe the FGS. Can be used as input to runBatchGSE.

Usage

 data(fgsList) 

Format

This object is a list of length two:

"go": this is a list of 5 character vectors, corresponding to 5 distinct Gene Ontology (GO) terms. Genes annotated to each GO term are identified by their gene symbol;

"kegg": this is a list of 5 character vectors, corresponding to 5 distinct KEGG pathways. Genes annotated to each KEGG pathway are identified by their gene symbol;

Source

The FGS were obtained from the org.Hs.eg.db pakage, (use the org.Hs.eg function to see the content); These FGS were annotated using data from GO.db and KEGGREST packages (use the GO and keggGet functions to see the content).

Examples

data(fgsList)
class(fgsList)
names(fgsList)
str(fgsList)

marchionniLab/RTopper documentation built on Oct. 29, 2022, 8:14 a.m.