BSgenome (version 1.36.3)

GenomeDataList-class: List of GenomeData objects

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.

GenomeDataList is a list of GenomeData objects. It could be useful for storing data on multiple experiments or samples.

Constructor

GenomeDataList(listData = list(), metadata = list(), elementMetadata = NULL): Creates a GenomeDataList with the elements from the listData parameter, a list of GenomeData instances. The other arguments correspond to the optional metadata stored in SimpleList.

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

Details

This class inherits from SimpleList and requires that all of its elements to be instances of GenomeData.

One should try to take advantage of the metadata storage facilities provided by SimpleList. The elementMetadata field, for example, could be used to store the experimental design, while the metadata field could store the experimental platform.

See Also

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

GenomeData, the type of elements stored in this class.

SimpleList

Examples

## Not run: 
# gd <- GenomeData(list(chr1 = IRanges(1, 10), chrX = IRanges(2, 5)),
#                  organism = "Mmusculus", provider = "UCSC",
#                  providerVersion = "mm9")
# gdl <- GenomeDataList(list(gd), elementMetadata = DataFrame(induced = TRUE))
# gdl[[1]] # get first element
# ## End(Not run)