catmap {systemPipeR} | R Documentation

## catDB accessor methods

### Description

Methods to access information from `catDB` object.

### Usage

    	catmap(x)

### Arguments

`x` | object of class `catDB`

### Value

various outputs

### Author(s)

Thomas Girke

### Examples

    ## Not run:
    ## Obtain annotations from BioMart
    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

    ## Access methods for catDB
    catmap(catdb)$D_MF[1:4,]
    catlist(catdb)$L_MF[1:4]
    idconv(catdb)

    ## End(Not run)

[Package systemPipeR version 1.22.0 Index]