GenomeData-class: Data on the genome
In Przemol/mirrors-bioc-BSgenome: Infrastructure for Biostrings-based genome data packages

Description Details Accessor methods Constructor Coercion Author(s) See Also Examples

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

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).

In the code snippets below, x is a GenomeData object.

: organism(x): 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.

: 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.

: 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.

Michael Lawrence

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.

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