ExperimentHubMetadata-class: Class ExperimentHubMetadata objects and methods

Description Usage Arguments Details Value See Also Examples

Description

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

Usage

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ExperimentHubMetadata(ExperimentHubRoot=NA_character_, 
        BiocVersion=biocVersion(),
        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='http://s3.amazonaws.com/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.

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.

TaxonomyId

character(1) NCBI code.

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(1) File path to where object is stored in AWS S3 bucket or on the web.

Maintainer

character(1) Maintainer name and email address, ‘A Maintainer [email protected]

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 [email protected] if you are not sure which class to use.

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

Examples

1
showClass("ExperimentHubMetadata")

ExperimentHubData documentation built on Nov. 17, 2017, 1:18 p.m.