setops-methods {GenomicRanges} | R Documentation

## Set operations on genomic ranges

### Description

Performs set operations on GRanges and GRangesList objects.

NOTE: The `punion`, `pintersect`, `psetdiff`, and `pgap` generic functions and methods for IntegerRanges objects are defined and documented in the IRanges package.

### Usage

    ## Vector-wise set operations
    ## --------------------------

    ## S4 method for signature 'GenomicRanges,GenomicRanges'
    union(x, y, ignore.strand=FALSE)

    ## S4 method for signature 'GenomicRanges,GenomicRanges'
    intersect(x, y, ignore.strand=FALSE)

    ## S4 method for signature 'GenomicRanges,GenomicRanges'
    setdiff(x, y, ignore.strand=FALSE)

    ## Element-wise (aka "parallel") set operations
    ## --------------------------------------------

    ## S4 method for signature 'GRanges,GRanges'
    punion(x, y, fill.gap=FALSE, ignore.strand=FALSE)

    ## S4 method for signature 'GRanges,GRanges'
    pintersect(x, y, drop.nohit.ranges=FALSE,
               ignore.strand=FALSE, strict.strand=FALSE)

    ## S4 method for signature 'GRanges,GRanges'
    psetdiff(x, y, ignore.strand=FALSE)

### Arguments

`x, y` | For `union`, `intersect`, and `setdiff`: 2 GenomicRanges objects or 2 GRangesList objects. For `punion` and `pintersect`: 2 GRanges objects, or 1 GRanges object and 1 GRangesList object. For `psetdiff`: `x` must be a GRanges object and `y` can be a GRanges or GRangesList object. For `pgap`: 2 GRanges objects. In addition, for the parallel operations, `x` and `y` must be of equal length (i.e. `length(x) == length(y)`).
`fill.gap` | Logical indicating whether or not to force a union by using the rule `start = min(start(x), start(y)), end = max(end(x), end(y))`.
`ignore.strand` | For set operations: If set to TRUE, then the strand of `x` and `y` is set to `"*"` prior to any computation. For parallel set operations: If set to TRUE, the strand information is ignored in the computation and the result has the strand information of `x`.
`drop.nohit.ranges` | If TRUE then elements in `x` that don't intersect with their corresponding element in `y` are removed from the result (so the returned object is no more parallel to the input). If FALSE (the default) then nothing is removed and a `hit` metadata column is added to the returned object to indicate elements in `x` that intersect with the corresponding element in `y`. For those that don't, the reported intersection is a zero-width range that has the same start as `x`.
`strict.strand` | If set to FALSE (the default), features on the `"*"` strand are treated as occurring on both the `"+"` and `"-"` strand. If set to TRUE, the strand of intersecting elements must be strictly the same.

### Details

The `pintersect` methods involving GRanges and/or GRangesList objects use the triplet (sequence name, range, strand) to determine the element by element intersection of features, where a strand value of `"*"` is treated as occurring on both the `"+"` and `"-"` strand (unless `strict.strand` is set to TRUE, in which case the strand of intersecting elements must be strictly the same).

The `psetdiff` methods involving GRanges and/or GRangesList objects use the triplet (sequence name, range, strand) to determine the element by element set difference of features, where a strand value of `"*"` is treated as occurring on both the `"+"` and `"-"` strand.

### Value

For `union`, `intersect`, and `setdiff`: a GRanges object if `x` and `y` are GenomicRanges objects, and a GRangesList object if they are GRangesList objects.

For `punion` and `pintersect`: when `x` or `y` is not a GRanges object, an object of the same class as this non-GRanges object. Otherwise, a GRanges object.

For `psetdiff`: either a GRanges object when both `x` and `y` are GRanges objects, or a GRangesList object when `y` is a GRangesList object.

For `pgap`: a GRanges object.

### Author(s)

P. Aboyoun and H. Pagès

### See Also

- setops-methods in the IRanges package for set operations on IntegerRanges and IntegerRangesList objects.

- findOverlaps-methods for finding/counting overlapping genomic ranges.

- intra-range-methods and inter-range-methods for intra range and inter range transformations of a GRanges object.

- GRanges and GRangesList objects.

- `mendoapply` in the S4Vectors package.

### Examples

    ## ---------------------------------------------------------------------
    ## A. SET OPERATIONS
    ## ---------------------------------------------------------------------

    x <- GRanges("chr1", IRanges(c(2, 9) , c(7, 19)), strand=c("+", "-"))
    y <- GRanges("chr1", IRanges(5, 10), strand="-")

    union(x, y)
    union(x, y, ignore.strand=TRUE)

    intersect(x, y)
    intersect(x, y, ignore.strand=TRUE)

    setdiff(x, y)
    setdiff(x, y, ignore.strand=TRUE)

    ## With 2 GRangesList objects:
    gr1 <- GRanges(seqnames="chr2",
                   ranges=IRanges(3, 6))
    gr2 <- GRanges(seqnames=c("chr1", "chr1"),
                   ranges=IRanges(c(7,13), width = 3),
                   strand=c("+", "-"))
    gr3 <- GRanges(seqnames=c("chr1", "chr2"),
                   ranges=IRanges(c(1, 4), c(3, 9)),
                   strand=c("-", "-"))
    grlist <- GRangesList(gr1=gr1, gr2=gr2, gr3=gr3)

    union(grlist, shift(grlist, 3))
    intersect(grlist, shift(grlist, 3))
    setdiff(grlist, shift(grlist, 3))

    ## Sanity checks:
    grlist2 <- shift(grlist, 3)
    stopifnot(identical(
        union(grlist, grlist2),
        mendoapply(union, grlist, grlist2)
    ))
    stopifnot(identical(
        intersect(grlist, grlist2),
        mendoapply(intersect, grlist, grlist2)
    ))
    stopifnot(identical(
        setdiff(grlist, grlist2),
        mendoapply(setdiff, grlist, grlist2)
    ))

    ## ---------------------------------------------------------------------
    ## B. PARALLEL SET OPERATIONS
    ## ---------------------------------------------------------------------

    punion(x, shift(x, 6))
    ## Not run:
    punion(x, shift(x, 7))  # will fail

    ## End(Not run)
    punion(x, shift(x, 7), fill.gap=TRUE)

    pintersect(x, shift(x, 6))
    pintersect(x, shift(x, 7))

    psetdiff(x, shift(x, 7))

    ## ---------------------------------------------------------------------
    ## C. MORE EXAMPLES
    ## ---------------------------------------------------------------------

    ## GRanges object:
    gr <- GRanges(seqnames=c("chr2", "chr1", "chr1"),
                  ranges=IRanges(1:3, width = 12),
                  strand=Rle(strand(c("-", "*", "-"))))

    ## Parallel intersection of a GRanges and a GRangesList object
    pintersect(gr, grlist)
    pintersect(grlist, gr)

    ## For a fast 'mendoapply(intersect, grlist, as(gr, "GRangesList"))'
    ## call pintersect() with 'strict.strand=TRUE' and call reduce() on
    ## the result with 'drop.empty.ranges=TRUE':
    reduce(pintersect(grlist, gr, strict.strand=TRUE),
           drop.empty.ranges=TRUE)

    ## Parallel set difference of a GRanges and a GRangesList object
    psetdiff(gr, grlist)

[Package GenomicRanges version 1.39.3 Index]