catmap | R Documentation |
Methods to access information from catDB
object.
catmap(x)
x |
object of class |
various outputs
Thomas Girke
## 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)
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