intra-tuple-methods {GenomicTuples} | R Documentation

## Intra-tuple transformations of a GTuples or GTuplesLists object

### Description

This man page documents intra-tuple transformations of a `GTuples` or a `GTuplesList` object.

WARNING: These are not exactly the same as the intra-range methods defined in the GenomicRanges package (`?GenomicRanges::intra-range-methods`) or in the IRanges package (`?IRanges::intra-range-methods`).

### Usage

    ## S4 method for signature 'GTuples'
    shift(x, shift = 0L, use.names = TRUE)
    ## S4 method for signature 'GTuplesList'
    shift(x, shift = 0L, use.names = TRUE)

    ## S4 method for signature 'GTuples'
    trim(x, use.names = TRUE)

### Arguments

`x` | A `GTuples` or `GTuplesList` object.
`shift, use.names` | See `?`intra-range-methods``.

### Details

- `shift` behaves like the `shift` method for GRanges objects, except that any `internalPos` are also shifted. See `?`intra-range-methods`` for further details of the `shift` method.

- `trim` trims out-of-bound tuples located on non-circular sequences whose length is not NA.

### Value

See Details section above.

### Author(s)

Peter Hickey for methods involving `GTuples` and `GTuplesList`. P. Aboyoun and V. Obenchain <vobencha@fhcrc.org> for all the real work underlying the powerful intra-range methods.

### See Also

- `GTuples` and `GTuplesList` objects.

- The intra-range-methods man page in the GenomicRanges package.

### Examples

    ## ---------------------------------------------------------------------
    ## A. ON A GTuples OBJECT
    ## ---------------------------------------------------------------------
    gt3 <- GTuples(seqnames = c('chr1', 'chr1', 'chr1', 'chr1', 'chr2'),
                   tuples = matrix(c(10L, 10L, 10L, 10L, 10L, 20L, 20L, 20L, 25L,
                                     20L, 30L, 30L, 35L, 30L, 30L), ncol = 3),
                   strand = c('+', '-', '*', '+', '+'))
    gt3

    shift(gt3, 10)

    ## ---------------------------------------------------------------------
    ## B. ON A GTuplesList OBJECT
    ## ---------------------------------------------------------------------
    gtl3 <- GRangesList(A = gt3, B = rev(gt3))
    gtl3

    shift(gtl3, IntegerList(10, 100))

[Package GenomicTuples version 1.21.5 Index]