Make a OrganismDb object from annotations available on a BioMart database

Description

The makeOrganismDbFromBiomart function allows the user to make a OrganismDb object from transcript annotations available on a BioMart database. This object has all the benefits of a TxDb, plus an associated OrgDb and GODb object.

Usage

makeOrganismDbFromBiomart(biomart="ENSEMBL_MART_ENSEMBL",
                    dataset="hsapiens_gene_ensembl",
                    transcript_ids=NULL,
                    circ_seqs=DEFAULT_CIRC_SEQS,
                    filter="",
                    id_prefix="ensembl_",
                    host="www.ensembl.org",
                    port=80,
                    miRBaseBuild=NA,
                    keytype = "ENSEMBL")

Arguments

Details

makeOrganismDbFromBiomart is a convenience function that feeds data from a BioMart database to the lower level OrganismDb constructor. See ?makeOrganismDbFromUCSC for a similar function that feeds data from the UCSC source.

The listMarts function from the biomaRt package can be used to list all public BioMart databases. Not all databases returned by this function contain datasets that are compatible with (i.e. understood by) makeOrganismDbFromBiomart. Here is a list of datasets known to be compatible (updated on Sep 24, 2014):

• All the datasets in the main Ensembl database: use biomart="ensembl".

• All the datasets in the Ensembl Fungi database: use biomart="fungi_mart_XX" where XX is the release version of the database e.g. "fungi_mart_22".

• All the datasets in the Ensembl Metazoa database: use biomart="metazoa_mart_XX" where XX is the release version of the database e.g. "metazoa_mart_22".

• All the datasets in the Ensembl Plants database: use biomart="plants_mart_XX" where XX is the release version of the database e.g. "plants_mart_22".

• All the datasets in the Ensembl Protists database: use biomart="protists_mart_XX" where XX is the release version of the database e.g. "protists_mart_22".

• All the datasets in the Gramene Mart: use biomart="ENSEMBL_MART_PLANT".

Not all these datasets have CDS information.

Value

A OrganismDb object.

Author(s)

M. Carlson and H. Pages

See Also

• makeOrganismDbFromUCSC for convenient ways to make a OrganismDb object from UCSC online resources.

• The listMarts, useMart, and listDatasets functions in the biomaRt package.

• DEFAULT_CIRC_SEQS.

• The supportedMiRBaseBuildValues function for listing all the possible values for the miRBaseBuild argument.

• The OrganismDb class.

Examples

## Discover which datasets are available in the "ensembl" BioMart
## database:
library(biomaRt)
head(listDatasets(useMart("ensembl")))

## Retrieving an incomplete transcript dataset for Human from the
## "ensembl" BioMart database:
transcript_ids <- c(
    "ENST00000013894",
    "ENST00000268655",
    "ENST00000313243",
    "ENST00000435657",
    "ENST00000384428",
    "ENST00000478783"
)
odb <- makeOrganismDbFromBiomart(transcript_ids=transcript_ids)
odb  # note that these annotations match the GRCh38 genome assembly

## Now what if we want to use another mirror?  We might make use of the
## new host argument.  But wait!  If we use biomaRt, we can see that
## this host has named the mart differently!
listMarts(host="uswest.ensembl.org")
## Therefore we must also change the name passed into the "mart"
## argument thusly:
try(
    odb <- makeOrganismDbFromBiomart(biomart="ENSEMBL_MART_ENSEMBL",
                                     transcript_ids=transcript_ids,
                                     host="uswest.ensembl.org")	    
)
odb

Results

R version 3.3.1 (2016-06-21) -- "Bug in Your Hair"
Copyright (C) 2016 The R Foundation for Statistical Computing
Platform: x86_64-pc-linux-gnu (64-bit)

R is free software and comes with ABSOLUTELY NO WARRANTY.
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Type 'license()' or 'licence()' for distribution details.

R is a collaborative project with many contributors.
Type 'contributors()' for more information and
'citation()' on how to cite R or R packages in publications.

Type 'demo()' for some demos, 'help()' for on-line help, or
'help.start()' for an HTML browser interface to help.
Type 'q()' to quit R.

> library(OrganismDbi)
Loading required package: BiocGenerics
Loading required package: parallel

Attaching package: 'BiocGenerics'

The following objects are masked from 'package:parallel':

    clusterApply, clusterApplyLB, clusterCall, clusterEvalQ,
    clusterExport, clusterMap, parApply, parCapply, parLapply,
    parLapplyLB, parRapply, parSapply, parSapplyLB

The following objects are masked from 'package:stats':

    IQR, mad, xtabs

The following objects are masked from 'package:base':

    Filter, Find, Map, Position, Reduce, anyDuplicated, append,
    as.data.frame, cbind, colnames, do.call, duplicated, eval, evalq,
    get, grep, grepl, intersect, is.unsorted, lapply, lengths, mapply,
    match, mget, order, paste, pmax, pmax.int, pmin, pmin.int, rank,
    rbind, rownames, sapply, setdiff, sort, table, tapply, union,
    unique, unsplit

Loading required package: AnnotationDbi
Loading required package: stats4
Loading required package: Biobase
Welcome to Bioconductor

    Vignettes contain introductory material; view with
    'browseVignettes()'. To cite Bioconductor, see
    'citation("Biobase")', and for packages 'citation("pkgname")'.

Loading required package: IRanges
Loading required package: S4Vectors

Attaching package: 'S4Vectors'

The following objects are masked from 'package:base':

    colMeans, colSums, expand.grid, rowMeans, rowSums

Loading required package: GenomicFeatures
Loading required package: GenomeInfoDb
Loading required package: GenomicRanges
> png(filename="/home/ddbj/snapshot/RGM3/R_BC/result/OrganismDbi/makeOrganismDbFromBiomart.Rd_%03d_medium.png", width=480, height=480)
> ### Name: makeOrganismDbFromBiomart
> ### Title: Make a OrganismDb object from annotations available on a BioMart
> ###   database
> ### Aliases: makeOrganismDbFromBiomart
> 
> ### ** Examples
> 
> ## Discover which datasets are available in the "ensembl" BioMart
> ## database:
> library(biomaRt)
> head(listDatasets(useMart("ensembl")))
                         dataset                                description
1         oanatinus_gene_ensembl     Ornithorhynchus anatinus genes (OANA5)
2        cporcellus_gene_ensembl            Cavia porcellus genes (cavPor3)
3        gaculeatus_gene_ensembl     Gasterosteus aculeatus genes (BROADS1)
4 itridecemlineatus_gene_ensembl Ictidomys tridecemlineatus genes (spetri2)
5         lafricana_gene_ensembl         Loxodonta africana genes (loxAfr3)
6        choffmanni_gene_ensembl        Choloepus hoffmanni genes (choHof1)
  version
1   OANA5
2 cavPor3
3 BROADS1
4 spetri2
5 loxAfr3
6 choHof1
> 
> ## Retrieving an incomplete transcript dataset for Human from the
> ## "ensembl" BioMart database:
> transcript_ids <- c(
+     "ENST00000013894",
+     "ENST00000268655",
+     "ENST00000313243",
+     "ENST00000435657",
+     "ENST00000384428",
+     "ENST00000478783"
+ )
> odb <- makeOrganismDbFromBiomart(transcript_ids=transcript_ids)
Download and preprocess the 'transcripts' data frame ... OK
Download and preprocess the 'chrominfo' data frame ... OK
Download and preprocess the 'splicings' data frame ... OK
Download and preprocess the 'genes' data frame ... OK
Prepare the 'metadata' data frame ... OK
Make the TxDb object ... OK


> odb  # note that these annotations match the GRCh38 genome assembly
OrganismDb Object:
# Includes GODb Object:  GO.db 
# With data about:  Gene Ontology 
# Includes OrgDb Object:  org.Hs.eg.db 
# Gene data about:  Homo sapiens 
# Taxonomy Id:  9606 
# Includes TxDb Object:  TxDb.Hsapiens.BioMart.ENSEMBLMARTENSEMBL.GRCh38.p5 
# Transcriptome data about:  Homo sapiens 
# Based on genome:   
# The OrgDb gene id ENSEMBL is mapped to the TxDb gene id GENEID .
> 
> ## Now what if we want to use another mirror?  We might make use of the
> ## new host argument.  But wait!  If we use biomaRt, we can see that
> ## this host has named the mart differently!
> listMarts(host="uswest.ensembl.org")
               biomart               version
1 ENSEMBL_MART_ENSEMBL      Ensembl Genes 84
2     ENSEMBL_MART_SNP  Ensembl Variation 84
3 ENSEMBL_MART_FUNCGEN Ensembl Regulation 84
4    ENSEMBL_MART_VEGA               Vega 64
> ## Therefore we must also change the name passed into the "mart"
> ## argument thusly:
> try(
+     odb <- makeOrganismDbFromBiomart(biomart="ENSEMBL_MART_ENSEMBL",
+                                      transcript_ids=transcript_ids,
+                                      host="uswest.ensembl.org")	    
+ )
Download and preprocess the 'transcripts' data frame ... OK
Download and preprocess the 'chrominfo' data frame ... OK
Download and preprocess the 'splicings' data frame ... OK
Download and preprocess the 'genes' data frame ... OK
Prepare the 'metadata' data frame ... OK
Make the TxDb object ... OK
> odb
OrganismDb Object:
# Includes GODb Object:  GO.db 
# With data about:  Gene Ontology 
# Includes OrgDb Object:  org.Hs.eg.db 
# Gene data about:  Homo sapiens 
# Taxonomy Id:  9606 
# Includes TxDb Object:  TxDb.Hsapiens.BioMart.ENSEMBLMARTENSEMBL.GRCh38.p5 
# Transcriptome data about:  Homo sapiens 
# Based on genome:   
# The OrgDb gene id ENSEMBL is mapped to the TxDb gene id GENEID .
> 
> 
> 
> 
> 
> dev.off()
null device 
          1 
>