Intra-tuple transformations of a GTuples or GTuplesLists object

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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

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## 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`.

...

Additional arguments to 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

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## ---------------------------------------------------------------------
## 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))