catDB-class: Class '"catDB"'
In systemPipeR: systemPipeR: NGS workflow and report generation environment

Description Objects from the Class Slots Methods Author(s) See Also Examples

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

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

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

Thomas Girke

makeCATdb, GOHyperGAll, GOHyperGAll_Subset, GOHyperGAll_Simplify, GOCluster_Report, goBarplot

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)