bbBuiltInDB: Get pre build biobtree database

In biobtreeR: Using biobtree tool from R

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

biobtreeR documentation built on Nov. 8, 2020, 5:19 p.m.