topAnat: Produces an object allowing to perform GO-like enrichment of...

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

Produces an object allowing to perform GO-like enrichment of anatomical terms using the topGO package

Description

This function produces a topAnatObject, ready to use for gene set enrichment testing using functions from the topGO package. This object uses the Uberon ontology instead of the GO ontology.

Usage

topAnat(topAnatData, geneList, nodeSize = 10, ...)

Arguments

topAnatData	a list including a gene2anatomy list, an organ.relationships list and an organ.names data.frame, produced by the function loadTopAnatData().
geneList	Vector indicating foreground and background genes. Names of the vector indicate the background genes. Values are 1 (gene in foreground) or 0 (gene not in foreground).
nodeSize	Minimum number of genes mapped to a node for it to be tested. Default is 10.
...	Additional parameters as passed to build topGOdata object in topGO package.

Details

To perform the enrichment test for expression in anatomical structures for each term of Uberon ontology (browsable at http://www.ontobee.org/ontology/UBERON), the data are formatted to use the topGO package for testing. This package is interesting because it propagates the mapping of gene to terms to parent terms, and it possesses a pannel of enrichment tests and decorrelation methods. Expert users should be able to use information from the topAnatObject to test enrichment with other packages than topGO.

Value

topAnatObject, a topAnatData class object, ready for gene set enrichment testing with topGO.

Author(s)

Julien Roux

Examples

{
bgee <- Bgee$new(species="Bos_taurus", dataType="rna_seq")
myTopAnatData <- loadTopAnatData(bgee, stage="UBERON:0000092")
geneList <- as.factor(c(rep(0, times=85), rep(1, times=15)))
names(geneList) <- c("ENSBTAG00000000011","ENSBTAG00000000014","ENSBTAG00000000016",
                     "ENSBTAG00000000026","ENSBTAG00000000039","ENSBTAG00000000040",
                     "ENSBTAG00000000042","ENSBTAG00000000050","ENSBTAG00000000056",
                     "ENSBTAG00000000064","ENSBTAG00000000067","ENSBTAG00000000071",
                     "ENSBTAG00000000072","ENSBTAG00000000080","ENSBTAG00000000081",
                     "ENSBTAG00000000084","ENSBTAG00000000091","ENSBTAG00000000099",
                     "ENSBTAG00000000111","ENSBTAG00000000123","ENSBTAG00000000132",
                     "ENSBTAG00000000153","ENSBTAG00000000162","ENSBTAG00000000163",
                     "ENSBTAG00000000169","ENSBTAG00000000179","ENSBTAG00000000197",
                     "ENSBTAG00000000199","ENSBTAG00000000202","ENSBTAG00000000203",
                     "ENSBTAG00000000204","ENSBTAG00000000213","ENSBTAG00000000215",
                     "ENSBTAG00000000223","ENSBTAG00000000224","ENSBTAG00000000225",
                     "ENSBTAG00000000236","ENSBTAG00000000250","ENSBTAG00000000251",
                     "ENSBTAG00000000252","ENSBTAG00000000253","ENSBTAG00000000261",
                     "ENSBTAG00000000274","ENSBTAG00000000277","ENSBTAG00000000279",
                     "ENSBTAG00000000285","ENSBTAG00000000286","ENSBTAG00000000287",
                     "ENSBTAG00000000289","ENSBTAG00000000297","ENSBTAG00000000305",
                     "ENSBTAG00000000312","ENSBTAG00000000328","ENSBTAG00000000335",
                     "ENSBTAG00000000341","ENSBTAG00000000343","ENSBTAG00000000354",
                     "ENSBTAG00000000355","ENSBTAG00000000356","ENSBTAG00000000365",
                     "ENSBTAG00000000372","ENSBTAG00000000379","ENSBTAG00000000380",
                     "ENSBTAG00000000382","ENSBTAG00000000396","ENSBTAG00000000404",
                     "ENSBTAG00000000405","ENSBTAG00000000406","ENSBTAG00000000411",
                     "ENSBTAG00000000425","ENSBTAG00000000434","ENSBTAG00000000435",
                     "ENSBTAG00000000438","ENSBTAG00000000448","ENSBTAG00000000451",
                     "ENSBTAG00000000454","ENSBTAG00000000456","ENSBTAG00000000457",
                     "ENSBTAG00000000459","ENSBTAG00000000462","ENSBTAG00000000469",
                     "ENSBTAG00000000470","ENSBTAG00000000484","ENSBTAG00000000497",
                     "ENSBTAG00000000501","ENSBTAG00000009707","ENSBTAG00000026266",
                     "ENSBTAG00000021992","ENSBTAG00000005353","ENSBTAG00000005333",
                     "ENSBTAG00000006424","ENSBTAG00000026972","ENSBTAG00000010799",
                     "ENSBTAG00000010799","ENSBTAG00000014614","ENSBTAG00000014614",
                     "ENSBTAG00000045757","ENSBTAG00000046332","ENSBTAG00000046332",
                     "ENSBTAG00000008394")
myTopAnatObject <-  topAnat(myTopAnatData, geneList)
}

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