Data on the genome

Description

WARNING: Starting with BioC 3.1, GenomeData and GenomeDataList objects are defunct. Note that the GenomeData/GenomeDataList containers predate the GRanges/GRangesList containers and, most of the times, the latters can be used instead of the formers. Please let us know on the bioc-devel mailing list (http://bioconductor.org/help/mailing-list/) if you have a use case where you think there are significant benefits in using GenomeData/GenomeDataList over GRanges/GRangesList, or if you have questions or concerns about this.

GenomeData formally represents genomic data as a list, with one element per chromosome in the genome.

Details

This class facilitates storing data on the genome by formalizing a set of metadata fields for storing the organism (e.g. Mmusculus), genome build provider (e.g. UCSC), and genome build version (e.g. mm9).

The data is represented as a list, with one element per chromosome (or really any sequence, like a gene). There are no constraints as to the data type of the elements.

Note that as a SimpleList, it is possible to store chromosome-level data (e.g. the lengths) in the elementMetadata slot. The organism, provider and providerVersion are all stored in the SimpleList metadata, so they may be retrieved in list form by calling metadata(x).

Accessor methods

In the code snippets below, object and x are GenomeData objects.

organism(object): Get the single string indicating the organism, if specified, otherwise NULL.

provider(x): Get the single string indicating the genome build provider, if specified, otherwise NULL.

providerVersion(x): Get the single string indicating the genome build version, if specified, otherwise NULL.

Constructor

GenomeData(listData = list(), providerVersion = metadata[["providerVersion"]], organism = metadata[["organism"]], provider = metadata[["provider"]], metadata = list(), elementMetadata = NULL, ...): Creates a GenomeData with the elements from the listData parameter, a list. The other arguments correspond to the metadata fields, and, with the exception of elementMetadata, should all be either single strings or NULL (unspecified). Additional global metadata elements may be passed in metadata, in list-form, and via .... The elements in metadata are always overridden by the explicit arguments, like organism and those in .... elementMetadata should be an DataTable or NULL.

Coercion

as(from, "data.frame"): Coerces each subelement to a data frame, and binds them into a single data frame with an additional column indicating chromosome

as(from, "RangesList"): Coerces each subelement to a Ranges and combines them into a RangesList with the same names. The “universe” metadata property is set to the providerVersion of from.

as(from, "RangedData"): Coerces each subelement to a RangedData and combines them into a single RangedData with the same names. The “universe” metadata property is set to the providerVersion of from.

Author(s)

Michael Lawrence

See Also

The GRanges and GRangesList classes defined and documented in the GenomicRanges package.

GenomeDataList-class, a container for storing a list of GenomeData objects and useful e.g. for storing data on multiple samples.

SimpleList-class, the base of this class.

gdapply for applying a function to elements of a GenomeData object.

gdReduce for successively combining GenomeData objects into a single GenomeData objects.

Examples

## Not run: 
gd <- GenomeData(list(chr1 = IRanges(1, 10), chrX = IRanges(2, 5)),
                 organism = "Mmusculus", provider = "UCSC",
                 providerVersion = "mm9")
organism(gd)
providerVersion(gd)
provider(gd)
gd[["chr1"]] # get data for chromsome 1

## End(Not run)