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

Description Usage Arguments Value Objects from the Class Author(s) Examples

Description

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

Usage

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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 =
                 "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 [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.

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

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getClass("AnnotationHubMetadata")

Bioconductor/AnnotationHubData documentation built on Aug. 14, 2018, 11:20 p.m.