AnnotationHubMetadata-class: Class '"AnnotationHubMetadata"' and methods

In Bioconductor/AnnotationHubData: Transform public data resources into Bioconductor Data Structures

Class "AnnotationHubMetadata" and methods

Description

AnnotationHubMetadata is used to represent record(s) in the server data base.

Usage

AnnotationHubMetadata(AnnotationHubRoot, SourceUrl, SourceType,
		 SourceVersion, SourceLastModifiedDate, SourceMd5 =
		 NA_character_, SourceSize, DataProvider, Title,
		 Description, Species, TaxonomyId, Genome, Tags,
		 Recipe, RDataClass, RDataDateAdded, RDataPath,
		 Maintainer, ..., BiocVersion = BiocManager::version(),
		 Coordinate_1_based = TRUE, Notes = NA_character_,
		 DispatchClass, Location_Prefix =
		 "https://bioconductorhubs.blob.core.windows.net/annotationhub/")

toJson(x)
constructSeqInfo(species, genome)

metadata(x, ...)
hubError(x)
inputFiles(object, ...)
outputFile(object)
ahmToJson(ahm)
deleteResources(id)
getImportPreparerClasses()
makeAnnotationHubResource(objName, makeAnnotationHubMetadataFunction,
			  ..., where)

Arguments

AnnotationHubRoot	character(1) Absolute path to directory structure containing resources to be added to AnnotationHub. 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() The date when the source was last modified.
SourceMd5	character() md5 hash of original file.
SourceSize	numeric(1) Size of original file in bytes.
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.
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. 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	character() Free-form tags that serve as search terms.
Recipe	character(1) Name of recipe function. Only applicable to recipes created by the Bioconductor core team and included in AnnotationHubData base code.
RDataClass	character() Class of derived R object, e.g., GRanges. Length must match the length of RDataPath.
RDataDateAdded	POSIXct() Date resource was added to AnnotationHub. 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.This field should be the remainder of the path to the resource. 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.
ahm	An instance of class AnnotationHubMetadata.
x	An instance of class AnnotationHubMetadata.
object	An AnnotationHubRecipe instance.
species	character(1) The organism, e.g., "Homo sapiens".
genome	character(1) The genome build, e.g., "hg19".
id	An id whose DB record is to be fully deleted.
objName	character(1) The name of the PreparerClass used for dispatch.
makeAnnotationHubMetadataFunction	function Function (name) that makes AnnotationHubMetadata objects from the resource(s).
where	Environment where function definition is defined. Default value is sufficient.
...	Additional arguments passed to methods.

Value

AnnotationHubMetadata returns an instance of the class.

jsonPath returns a character(1)) representation of the full path to the location of the json file associated with this record.

toJson returns the JSON representation of the record.

fromJson retuns an instance of the class, as parsed from the JSON file.

Objects from the Class

Objects can be created by calls to the constructor, AnnotationHubMetadata().

Author(s)

Dan Tenenbaum and Marc Carlson

Examples

getClass("AnnotationHubMetadata")

Bioconductor/AnnotationHubData documentation built on Oct. 31, 2024, 8:13 a.m.