R: Reduces arguments to a single GenomeData instance

gdReduce {BSgenome}

R Documentation

Reduces arguments to a single GenomeData instance

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.

This function accepts one or more objects that are reduced, with a user-specified function, to a single GenomeData instance.

Usage

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

Arguments

`f`	An object of class `"function"`, accepting two instances of classes appropriate for the `...` arguments, and returning an object suitable for subsequent use in `f` and incorporation into `GenomeData`.
`...`	Objects to be reduced. All objects should be of the same class, as dictated by methods defined on `gdReduce` A function to be applied to each chromosome-level sub-element of `X`.
`init`	An R object of the same kind as the elements of ....
`right`	A logical indicating whether to proceed from left to right (default) or right to left.
`accumulate`	A logical indicating whether the successive reduce combinations should be accumulated. By default, only the final combination is used.
`gdArgs`	Additional arguments passed to the `GenomeData` constructor used to assemble the final object.

Details

The gdReduce method for GenomeData objects successively combines GenomeData elements of ... using f; all arguments assigned to ... must be of class GenomeData. f is a function accepting two objects returned by "[[" applied to the successive 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.

Currently the gdReduce method for GenomeDataList objects works when a single GenomeDataList object x is provided as ... and it does gdReduce(f, x[[1]], x[[2]] ... x[[N]], init, right, accumulate, gdArgs) where N is the length of x i.e. the number of GenomeData objects in it.

Value

An object of class GenomeData, containing elements corresponding to the intersection of all named elements of ... (in the case of the method for GenomeData objects) or all elements in the single GenomeDataList object passed to it (in the case of the method for GenomeDataList objects).

Author(s)

Martin Morgan

Examples

## Not run: 
gdReduce
showMethods("gdReduce")

gd <- GenomeData(list(chr1 = IRanges(1, 10), chrX = IRanges(2, 5)),
                 organism = "Mmusculus", provider = "UCSC",
                 providerVersion = "mm9")

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"]]

## End(Not run)

[Package BSgenome version 1.36.2 Index]