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", ...).

Slots

catmap:

Object of class "list" list of data.frames

catlist:

Object of class "list" list of lists

idconv:

Object of class "ANY" list of data.frames

Methods

catlist

signature(x = "catDB"): extracts data from catlist slot

catmap

signature(x = "catDB"): extracts data from catmap slot

coerce

signature(from = "list", to = "catDB"): as(list, "catDB")

idconv

signature(x = "catDB"): extracts data from idconv slot

names

signature(x = "catDB"): extracts slot names

show

signature(object = "catDB"): summary view of catDB objects

Author(s)

Thomas Girke

See Also

makeCATdb, GOHyperGAll, GOHyperGAll_Subset, GOHyperGAll_Simplify, GOCluster_Report, goBarplot

Examples

showClass("catDB")
## Not run: 
## 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

## End(Not run)