RleViewsList-class {IRanges} | R Documentation

## List of RleViews

### Description

An extension of ViewsList that holds only RleViews objects. Useful for storing coverage vectors over a set of spaces (e.g. chromosomes), each of which requires a separate RleViews object.

### Details

For more information on methods available for RleViewsList objects consult the man pages for ViewsList-class and view-summarization-methods.

### Constructor

  `RleViewsList(..., rleList, rangesList)`: Either `...` or the `rleList`/`rangesList` couplet provide the RleViews for the list. If `...` is provided, each of these arguments must be RleViews objects. Alternatively, `rleList` and `rangesList` accept Rle and IntegerRanges objects respectively that are meshed together for form the RleViewsList.

  `Views(subject, start=NULL, end=NULL, width=NULL, names=NULL)`: Same as `RleViewsList(rleList = subject, rangesList = start)`.

### Coercion

In the code snippet below, `from` is an RleViewsList object:

  `as(from, "IRangesList")`: Creates an `IRangesList` object containing the view locations in `from`.

### Author(s)

P. Aboyoun

### See Also

ViewsList-class, view-summarization-methods

### Examples

    ## Rle objects
    subject1 <- Rle(c(3L,2L,18L,0L), c(3,2,1,5))
    set.seed(0)
    subject2 <- Rle(c(0L,5L,2L,0L,3L), c(8,5,2,7,4))

    ## Views
    rleViews1 <- Views(subject1, 3:0, 5:8)
    rleViews2 <- Views(subject2, subject2 > 0)

    ## RleList and IntegerRangesList objects
    rleList <- RleList(subject1, subject2)
    rangesList <- IRangesList(IRanges(3:0, 5:8), IRanges(subject2 > 0))

    ## methods for construction
    method1 <- RleViewsList(rleViews1, rleViews2)
    method2 <- RleViewsList(rleList = rleList, rangesList = rangesList)
    identical(method1, method2)

    ## calculation over the views
    viewSums(method1)

[Package IRanges version 2.14.12 Index]