BiocGenerics (version 0.18.0)

strand: Accessing strand information

Description

Get or set the strand information contained in an object.

Usage

strand(x, ...)
strand(x, ...) <- value
unstrand(x)
invertStrand(x)
"invertStrand"(x)

Arguments

x

An object containing strand information.

...

Additional arguments, for use in specific methods.

value

The strand information to set on x.

Value

If x is a vector-like object, strand(x) will typically return a vector-like object parallel to x, that is, an object of the same length as x where the i-th element describes the strand of the i-th element in x.unstrand(x) and invertStrand(x) return a copy of x with the strand set to "*" for unstrand or inverted for invertStrand (i.e. "+" and "-" switched, and "*" untouched).

Details

All the strand methods defined in the GenomicRanges package use the same set of 3 values (called the "standard strand levels") to specify the strand of a genomic location: +, -, and *. * is used when the exact strand of the location is unknown, or irrelevant, or when the "feature" at that location belongs to both strands.

Note that unstrand is not a generic function, just a convenience wrapper to the generic strand setter (strand<-) that does:

  strand(x) <- "*"
  x

The default method for invertStrand does:

  strand(x) <- invertStrand(strand(x))
  x

See Also

• showMethods for displaying a summary of the methods defined for a given generic function.

• selectMethod for getting the definition of a specific method.

• strand,GRanges-method in the GenomicRanges package for an example of a specific strand method (defined for GRanges objects).

• BiocGenerics for a summary of all the generics defined in the BiocGenerics package.

Examples

strand
showMethods("strand")

`strand<-`
showMethods("strand<-")

unstrand

invertStrand
showMethods("invertStrand")
selectMethod("invertStrand", "ANY")  # the default method

library(GenomicRanges)

showMethods("strand")
selectMethod("strand", "missing")
strand()

showMethods("strand<-")