bbBuiltInDB {biobtreeR}R Documentation

Get pre build biobtree database

Description

Pre build biobtree database for commonly studied datasets and model organism genomes. Once this function called it retrieves the pre build database saves to users output directory.

Usage

bbBuiltInDB(type = "1")

Arguments

type

built in database type accepted values are 1,2,3 and 4. Currently there are 4 different builtin database; Type 1 Requires ~ 5 GB free storage Included datasets hgnc,hmdb,taxonomy,go,efo,eco,chebi,interpro Included uniprot proteins and ensembl genomes belongs to following organisms

homo_sapiens 9606 –> ensembl danio_rerio 7955 zebrafish –> ensembl gallus_gallus 9031 chicken –> ensembl mus_musculus 10090 –> ensembl Rattus norvegicus 10116 —> ensembl saccharomyces_cerevisiae 4932–> ensembl,ensembl_fungi arabidopsis_thaliana 3702–> ensembl_plants drosophila_melanogaster 7227 –> ensembl,ensembl_metazoa caenorhabditis_elegans 6239 –> ensembl,ensembl_metazoa Escherichia coli 562 –> ensembl_bacteria Escherichia coli str. K-12 substr. MG1655 511145 –> ensembl_bacteria Escherichia coli K-12 83333 –> ensembl_bacteria

Type 2 Requires ~ 5 GB free storage Instead of genomes in in the type 1 it contains human and all the mouse strains genomes with their uniprot proteins. In addition hgnc,hmdb,taxonomy,go,efo,eco,chebi,interpro datasets are included

Type 3 Requires ~ 4 GB storage Contains no genome but it contains all the uniprot data with hgnc,hmdb,taxonomy,go,efo,eco,chebi,interpro

Type 4 Requires ~ 13 GB storage Contains no genome but full uniprot and chembl data with hgnc,hmdb,taxonomy,go,efo,eco,chebi,interpro

Value

returns empty

Author(s)

Tamer Gur

Examples


bbUseOutDir(tempdir()) # temp dir for demo purpose
bbBuiltInDB("demo") # small demo database for real database use 1, 2, 3 or 4



[Package biobtreeR version 1.6.0 Index]