makeStandardOrgDbs: Functions to add OrgDb and TxDb sqlite files to AnnotationHub

Description Usage Arguments Details Value Author(s) See Also Examples

Description

Add OrgDb and TxDb sqlite files to AnnotationHub

Usage

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makeStandardOrgDbsToAHM(currentMetadata, justRunUnitTest = FALSE, 
                        BiocVersion = BiocManager::version(), 
                        downloadOrgDbs = TRUE)

makeStandardTxDbsToAHM(currentMetadata, justRunUnitTest = FALSE, 
                       BiocVersion = BiocManager::version(), TxDbs)

makeNCBIToOrgDbsToAHM(currentMetadata, justRunUnitTest = FALSE,
                      BiocVersion = BiocManager::version(), 
                      baseUrl = "ftp://ftp.ncbi.nlm.nih.gov/gene/DATA/")

Arguments

currentMetadata

Historically was intended to be a list of metadata to filter, i.e., records that do not need to be processed again. In some recipes this is used as a way to pass additional arguments. Need to remove or make consistent.

baseUrl

A character(). The file location.

justRunUnitTest

A logical. When TRUE, a small number of records (usually <= 5) are processed instead of all.

BiocVersion

A character(1). The resource will be available for Bioconductor versions greater than and equal to this version. Default is BiocManaer::version().

TxDbs

Character vector of the TxDb names; generally includes TxDbs that were new or updated for the current release.

downloadOrgDbs

A logical. Indicates if all OrgDb packages in the Bioconductor repo should be downloaded and installed. This should be TRUE the first time the recipe is run and can be FALSE for subsequent runs when testing.

Details

makeStandardOrgDbsToAHM and makeStandardTxDbsToAHM extracts the sqlite files from the existing OrgDb and TxDb packages in the Bioconductor repositories and generate associated metadata.

makeNCBIToOrgDbsToAHM creates sqlite files and metadata for 1000 organisms with the makeOrgPackageFromNCBI function. These organisms are less 'main stream' than those hosted in the Bioconductor repository (makeStandardOrgDbsToAHM) and the databases are less comprehensive because data only come from one source, NCBI.

Value

List of AnnotationHubMetadata objects.

Author(s)

Bioconductor Core Team

See Also

Examples

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## Not run: 
## In Bioconductor 3.5, one new TxDb was added and 4 active
## tracks were updated. This piece of code shows how to add these 5
## packages to AnnotationHub.

## Step I: generate metadata 
##
## Generate the metadata with the low-level helper for inspection.
TxDbs <- c("TxDb.Ggallus.UCSC.galGal5.refGene",
           "TxDb.Celegans.UCSC.ce11.refGene",
           "TxDb.Rnorvegicus.UCSC.rn5.refGene",
           "TxDb.Dmelanogaster.UCSC.dm6.ensGene",
           "TxDb.Rnorvegicus.UCSC.rn6.refGene")
meta <- makeStandardTxDbsToAHM(currentMetadata=list(AnnotationHubRoot=getwd()), 
                               justRunUnitTest=FALSE, 
                               TxDbs = TxDbs)

## Once the low-level helper runs with no errors, try generating the
## metadata with the high-level wrapper updateResources(). Setting
## metadataOnly=TRUE will generate metadata only and not push resources
## to S3. insert=FALSE prevents the metadata from being inserted in the
## database.
##
## The metadata generated by updateResources() will be the same as that
## generated by makeStandardTxDbsToAHM(). Both should be a list the same
## length as the number of TxDbs specified.
meta <- updateResources(getwd(),
                        preparerClasses="TxDbFromPkgsImportPreparer",
                        metadataOnly=TRUE, insert = FALSE,
                        justRunUnitTest=FALSE, TxDbs = TxDbs)

INFO [2017-04-11 09:12:09] Preparer Class: TxDbFromPkgsImportPreparer
complete!
> length(meta)
[1] 5

## Step II: push resources to S3 
##
## If the metadata looks correct we are ready to push resources to S3.
## Set metadataOnly=FALSE but keep insert=FALSE.

meta <- updateResources(getwd(),
                        BiocVersion="3.5",
                        preparerClasses="TxDbFromPkgsImportPreparer",
                        metadataOnly=FALSE, insert = FALSE,
                        justRunUnitTest=FALSE, TxDbs = TxDbs)

## Step III: insert metadata in AnnotationHub production database
##
## Inserting the metadata in the database is usually done as a separte step
## and with the help of the AnnotationHub docker.
## Set metadataOnly=TRUE and insert=TRUE.
meta <- updateResources(getwd(),
                        BiocVersion="3.5",
                        preparerClasses="TxDbFromPkgsImportPreparer",
                        metadataOnly=FALSE, insert = FALSE,
                        justRunUnitTest=FALSE, TxDbs = TxDbs)


## End(Not run)

Bioconductor/AnnotationHubData documentation built on Oct. 14, 2018, 2:06 p.m.