catDB-class {systemPipeR} | R Documentation |
"catDB"
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
signature(x = "catDB")
: extracts data from catlist
slot
signature(x = "catDB")
: extracts data from catmap
slot
signature(from = "list", to = "catDB")
: as(list, "catDB")
signature(x = "catDB")
: extracts data from idconv
slot
signature(x = "catDB")
: extracts slot names
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)