geneList: Example of gene list object used to run a topAnat enrichment...

In BgeeDB/BgeeDB_R: Annotation and gene expression data retrieval from Bgee database. TopAnat, an anatomical entities Enrichment Analysis tool for UBERON ontology

Example of gene list object used to run a topAnat enrichment test, created on June 2018. The format of the gene list is the same as the gene list required to build a topGOdata object in the topGO package: a vector with background genes as names, and 0 or 1 values depending if a gene is in the foreground or not. In this example the foreground genes are zebrafish genes with an annotated phenotype related to "pectoral fin", and the background is composed of all zebrafish Ensembl genes with an annotated phenotype from ZFIN. The gene list was built using the biomaRt package, and the code used can be found in the vignette of the package.

Description

Example of gene list object used to run a topAnat enrichment test, created on June 2018. The format of the gene list is the same as the gene list required to build a topGOdata object in the topGO package: a vector with background genes as names, and 0 or 1 values depending if a gene is in the foreground or not. In this example the foreground genes are zebrafish genes with an annotated phenotype related to "pectoral fin", and the background is composed of all zebrafish Ensembl genes with an annotated phenotype from ZFIN. The gene list was built using the biomaRt package, and the code used can be found in the vignette of the package.

Usage

data(geneList)

Format

A named vector of factor values with 3005 elements. The factor levels are "0" for the 2858 genes in the background and "1" for the 147 genes in the foreground. Vector names are the Ensembl IDs of the zebrafish genes.

Examples

bgee <- Bgee$new(species = "Danio_rerio")
myTopAnatData <- loadTopAnatData(bgee)
data(geneList)
myTopAnatObject <-  topAnat(myTopAnatData, geneList)

BgeeDB/BgeeDB_R documentation built on Jan. 14, 2024, 4:29 a.m.