AnnotationHubMetadata-class {AnnotationHubData} | R Documentation

## 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 = biocVersion(),
                     Coordinate_1_based = TRUE, Notes = NA_character_,
                     DispatchClass, Location_Prefix =
                     "http://s3.amazonaws.com/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.
`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.
`TaxonomyId` | `character(1)` NCBI code
`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. Length must match the length of `RDataClass`.
`Maintainer` | `character(1)` Maintainer name and email address, ‘A Maintainer a.maintainer@email.com’
`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 maintainer@bioconductor.org 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.
`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")

[Package AnnotationHubData version 1.10.3 Index]