GenomeDataList-class {BSgenome}R Documentation

List of GenomeData objects

Description

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

Details

This is simply an AnnotatedList that requires all of its elements to be instances of GenomeData.

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

Constructor

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

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

Author(s)

Michael Lawrence

See Also

GenomeData, the type of elements stored in this class. AnnotatedList, the base of this class.

Examples

gd <- GenomeData(list(chr1 = IRanges(1, 10), chrX = IRanges(2, 5)),
                 organism = "Mmusculus", provider = "UCSC",
                 providerVersion = "mm9")
gdl <- GenomeDataList(list(gd), elementMetadata = XDataFrame(induced = TRUE))
gdl[[1]] # get first element

[Package BSgenome version 1.12.3 Index]