| GenomeData-class {BSgenome} | R Documentation |
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 an AnnotatedList, 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 the AnnotatedList
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(elements = list(), providerVersion = NULL,
organism = NULL, provider = NULL, metadata = list(),
elementMetadata = NULL, ...):
Creates a GenomeData with the elements from the
elements 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 XDataFrame
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
Michael Lawrence
GenomeDataList, a container of this class and useful for storing data on multiple samples.
AnnotatedList, the base of this class.
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