catmap: catDB accessor methods

In tgirke/systemPipeR: systemPipeR: Workflow Environment for Data Analysis and Report Generation

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)

tgirke/systemPipeR documentation built on June 13, 2025, 1:38 p.m.