systemPipeR (version 1.6.2)

catDB-class: Class "catDB"

Description

Container for storing mappings of genes to annotation categories such as gene ontologies (GO), pathways or conserved sequence domains. The catmap slot stores a list of data.frames providing the direct assignments of genes to annotation categories (e.g. gene-to-GO mappings); catlist is a list of lists of all direct and indirect associations to the annotation categories (e.g. genes mapped to a pathway); and idconv allows to store a lookup-table for converting identifiers (e.g. array feature ids to gene ids).

Objects from the Class

Objects can be created by calls of the form new("catDB", ...).

See Also

makeCATdb, GOHyperGAll, GOHyperGAll_Subset, GOHyperGAll_Simplify, GOCluster_Report, goBarplot

Examples

showClass("catDB")
## Obtain annotations from BioMart
listMarts() # To choose BioMart database
m <- useMart("ENSEMBL_MART_PLANT"); listDatasets(m) 
m <- useMart("ENSEMBL_MART_PLANT", dataset="athaliana_eg_gene")
listAttributes(m) # Choose data types you want to download
go <- getBM(attributes=c("go_accession", "tair_locus", "go_namespace_1003"), mart=m)
go <- go[go[,3]!="",]; go[,3] <- as.character(go[,3])
write.table(go, "GOannotationsBiomart_mod.txt", quote=FALSE, row.names=FALSE, col.names=FALSE, sep="\t")

## Create catDB instance (takes a while but needs to be done only once)
catdb <- makeCATdb(myfile="GOannotationsBiomart_mod.txt", lib=NULL, org="", colno=c(1,2,3), idconv=NULL)
catdb