ExperimentHubMetadata-class: Class ExperimentHubMetadata objects and methods

In Bioconductor/ExperimentHubData: Add resources to ExperimentHub

Class ExperimentHubMetadata objects and methods

Description

The ExperimentHubMetadata object is used to represent records in the server data base.

Usage

ExperimentHubMetadata(ExperimentHubRoot=NA_character_,
	BiocVersion=BiocManager::version(),
	SourceUrl=NA_character_,
	SourceType=NA_character_,
	SourceVersion=NA_character_,
	SourceLastModifiedDate=as.POSIXct(NA_character_),
	SourceMd5=NA_character_,
	SourceSize=NA_real_,
	DataProvider=NA_character_,
	Title=NA_character_,
	Description=NA_character_,
	Maintainer=NA_character_,
	Species=NA_character_,
	TaxonomyId=NA_integer_,
	Genome=NA_character_,
	Tags=NA_character_,
	RDataClass=NA_character_,
	RDataDateAdded=as.POSIXct(NA_character_),
	RDataPath=NA_character_,
	Coordinate_1_based=TRUE,
	Notes=NA_character_,
	DispatchClass=NA_character_,
	PreparerClass=NA_character_,
	Location_Prefix='https://bioconductorhubs.blob.core.windows.net/experimenthub/')

Arguments

ExperimentHubRoot	character(1) Prefix of the local path to resources to be added to ExperimentHub. Internal use only.
SourceUrl	character() URL of original resource(s).
SourceType	character() Form of original data, e.g., BED, FASTA, etc. getValidSourceTypes() list currently acceptable values. If nothing seems appropiate for your data reach out to [e-mail].
SourceVersion	character(1) Version of original file.
SourceLastModifiedDate	POSIXct() Date when resource was last modified.
SourceMd5	character(1) md5 hash of original file.
SourceSize	numeric(1) Number of bytes in original file.
DataProvider	character(1) Provider of original data, e.g., NCBI, UniProt etc.
Title	character(1) Title for the resource with version or genome build as appropriate. Titles must be unique and not match any existing title in ExperimentHub.
Description	character(1) Description of the resource. May include details such as data type, format, study origin, sequencing technology, treated vs control, number of samples etc.
Species	character(1) Species name.For help on valid species see getSpeciesList, validSpecies, or suggestSpecies.
TaxonomyId	character(1) NCBI code. Taxonomy ID. There are checks for valid taxonomyId given the Species which produce warnings. See GenomeInfoDb::loadTaxonomyDb() for full validation table.
Genome	character(1) Name of genome build.
Tags	‘Tags’ are search terms used to define a subset of resources in a Hub object, e.g, in a call to query. For ExperimentHub resources, ‘Tags’ are automatically generated from the ‘biocViews’ in the DESCRIPTION file of the accompanying software package. ‘Tags’ values supplied by the user are not be entered in the database and are not part of the formal metadata. This 'controlled vocabulary' approach was taken to limit the search terms to a well defined set and may change in the future.
RDataClass	character(1) Class of derived object (e.g. ‘GRanges’).
RDataDateAdded	POSIXct() Date resource was added to ExperimentHub. The default is today's date and is auto-generated when metadata are constructed. Resources will appear in snapshots with a date greater than or equal to the RDataDateAdded.
RDataPath	character() File path to where object is stored in AWS S3 bucket or on the web.The Location_Prefix will be prepended to RDataPath for the full path to the resource. If the resource is stored in Bioconductor's AWS S3 buckets, it should start with the name of the package associated with the metadata and should not start with a leading slash. It should include the resource file name. For strongly associated files, like a bam file and its index file, the two files should be separates with a colon :. This will link a single hub id with the multiple files.
Maintainer	character(1) Maintainer name and email address, ‘A Maintainer [e-mail]’
BiocVersion	character(1). The first Bioconductor version the resource was made available for. Unless removed from the hub, the resource will be available for all versions greater than or equal to this field.
Coordinate_1_based	logical(1) Do coordinates start with 1 or 0?
DispatchClass	character(1). Determines how data are loaded into R. The value for this field should be ‘Rda’ if the data were serialized with save() and ‘Rds’ if serialized with saveRDS. The filename should have the appropriate ‘rda’ or ‘rds’ extension. A number of dispatch classes are pre-defined in AnnotationHub/R/AnnotationHubResource-class.R with the suffix ‘Resource’. For example, if you have sqlite files, the AnnotationHubResource-class.R defines SQLiteFileResource so the DispatchClass would be SQLiteFile. Contact [e-mail] if you are not sure which class to use.The function AnnotationHub::DispatchClassList() will output a matrix of currently implemented DispatchClass and brief description of utility. If a predefine class does not seem appropriate contact [e-mail].
Location_Prefix	character(1) URL location of AWS S3 bucket or web site where resource is located.
Notes	character() Notes about the resource.
PreparerClass	character(1) Used internally.

Details

In practice, instances of this class are generated by a call to addResources or makeExperimentHubMetadata instead of a direct call to the constructor.

addResources is a function used by the Bioconductor Core team when adding new metadata records to the production database. makeExperimentHubMetadata and the low-level helper

Value

A ExperimentHubMetadata object.

See Also

• addResources

• makeExperimentHubMetadata

Examples

showClass("ExperimentHubMetadata")

Bioconductor/ExperimentHubData documentation built on Oct. 31, 2024, 7 a.m.