getTxDB: Search for TxDB

In DPP4ResearchGroup/SyntenyViz: Visualize the synteny of a gene structure across species

Search for TxDB

Description

Search if there is a corresponding annotation database TxDB is available for the given organism.

Usage

getTxDB(orgm, orgTxDB)

Arguments

orgm

An organism that of interest. Options include: Btaurus(Bt) - Bos taurus - Cow Celegans(Ce) - Caenorhabditis elegans - Roundworm Cfamiliaris(Cf) - Canis familiaris - Dog Dmelanogaster(Dm) - Drosophila melanogaster - Fruitfly Drerio(Dr) - Danio rerio - Zebrafish Ggallus(Gg) - Gallus gallus - Chicken Hsapiens(Hs) - Homo Sapiens - Human Mmulatta(Mmu) - Macaca mulatta - Rhesus macaque Mmusculus(Mm) - Mus musculus - House mouse Ptroglodytes(Pt) - Pan troglodytes - Chimpanzee Rnorvegicus(Rn) - Rattus norvegicus - Brown rat Scerevisiae(Sc) - Saccharomyces cerevisiae - Brewer's yeast Sscrofa(Ss) - Sus scrofa - Wild swine

orgTxDB

A data.frame that contains currently TxDB objects, e.g. orgmTxDB.

getDB complementing functions

A collection of complementing functions that required by the main functions: getPkgs , which includes following functions:

1. getOrgDB

2. getTxDB

See Also

Other orgTxDB: orgmTxDB

Other getDB: getOrgDB(), getPkgs()

Examples

orgm <- "Hsapiens"
getTxDB (orgm, orgmTxDB)

DPP4ResearchGroup/SyntenyViz documentation built on Nov. 19, 2023, 1:16 a.m.