Accessing strand information
Get or set the strand information contained in an object.
strand(x, ...) strand(x, ...) <- value unstrand(x) invertStrand(x) ## S4 method for signature 'ANY' invertStrand(x)
x |
An object containing strand information. |
... |
Additional arguments, for use in specific methods. |
value |
The strand information to set on |
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
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).
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.
strand
showMethods("strand")
`strand<-`
showMethods("strand<-")
unstrand
invertStrand
showMethods("invertStrand")
selectMethod("invertStrand", "ANY") # the default method
library(GenomicRanges)
showMethods("strand")
selectMethod("strand", "missing")
strand()
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