catDB-class {systemPipeR} | R Documentation

## 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)

[Package systemPipeR version 1.18.2 Index]