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 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.

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

Reduction

gdreduce(f, ..., init, right=FALSE, accumulate=FALSE, gdArgs=list()):

Currently this method works when a single GenomeDataList is provided as .... It successively combines the GenomeData elements in the GenomeDataList using f. f is a function accepting two objects returned by "[[" applied to the successive GenomeData elements of ..., returning a single GenomeData object to be used in subsequent calls to f. init, right, and accumulate are as described for Reduce. gdArgs can be used to provide metadata information to the constructor used to create the final GenomeData object.

Author(s)

Michael Lawrence

See Also

GenomeData, the type of elements stored in this class. SimpleList

Examples

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

gdr <- gdreduce(function(x, y) {
    ## "[[" returns IRanges instances, construct a synthetic version
    IRanges(c(start(x), start(y)), c(end(x), end(y)))
}, GenomeDataList(list(gd, gd[2])))
gdr[["chr1"]]
gdr[["chrX"]]