strand: Accessing strand information
In BiocGenerics: S4 generic functions used in Bioconductor

Description Usage Arguments Details Value See Also Examples

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 `x`.

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:

1 2	strand(x) <- "*" x

The default method for invertStrand does:

1 2	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()

showMethods("strand<-")

Loading required package: parallel

Attaching package: 'BiocGenerics'

The following objects are masked from 'package:parallel':

    clusterApply, clusterApplyLB, clusterCall, clusterEvalQ,
    clusterExport, clusterMap, parApply, parCapply, parLapply,
    parLapplyLB, parRapply, parSapply, parSapplyLB

The following objects are masked from 'package:stats':

    IQR, mad, xtabs

The following objects are masked from 'package:base':

    Filter, Find, Map, Position, Reduce, anyDuplicated, append,
    as.data.frame, cbind, colnames, do.call, duplicated, eval, evalq,
    get, grep, grepl, intersect, is.unsorted, lapply, lengths, mapply,
    match, mget, order, paste, pmax, pmax.int, pmin, pmin.int, rank,
    rbind, rownames, sapply, setdiff, sort, table, tapply, union,
    unique, unsplit, which, which.max, which.min

standardGeneric for "strand" defined from package "BiocGenerics"

function (x, ...) 
standardGeneric("strand")
<environment: 0x3ef7a10>
Methods may be defined for arguments: x
Use  showMethods("strand")  for currently available ones.
Function: strand (package BiocGenerics)
<No methods>

standardGeneric for "strand<-" defined from package "BiocGenerics"

function (x, ..., value) 
standardGeneric("strand<-")
<environment: 0x3f143e8>
Methods may be defined for arguments: x, value
Use  showMethods("strand<-")  for currently available ones.
Function: strand<- (package BiocGenerics)
<No methods>

function (x) 
{
    strand(x) <- "*"
    x
}
<environment: namespace:BiocGenerics>
standardGeneric for "invertStrand" defined from package "BiocGenerics"

function (x) 
standardGeneric("invertStrand")
<environment: 0x3e0a728>
Methods may be defined for arguments: x
Use  showMethods("invertStrand")  for currently available ones.
Function: invertStrand (package BiocGenerics)
x="ANY"

Method Definition:

function (x) 
{
    strand(x) <- invertStrand(strand(x))
    x
}
<environment: namespace:BiocGenerics>

Signatures:
        x    
target  "ANY"
defined "ANY"
Loading required package: stats4
Loading required package: S4Vectors

Attaching package: 'S4Vectors'

The following objects are masked from 'package:base':

    colMeans, colSums, expand.grid, rowMeans, rowSums

Loading required package: IRanges
Loading required package: GenomeInfoDb
Function: strand (package BiocGenerics)
x="DataTable"
x="DelegatingGenomicRanges"
x="GNCList"
x="GPos"
x="GRanges"
x="GRangesList"
x="NULL"
x="Rle"
x="RleList"
x="character"
x="factor"
x="integer"
x="logical"
x="missing"

Method Definition:

function (x, ...) 
{
    .local <- function (x) 
    factor(levels = c("+", "-", "*"))
    .local(x, ...)
}
<environment: namespace:GenomicRanges>

Signatures:
        x        
target  "missing"
defined "missing"
factor(0)
Levels: + - *
Function: strand<- (package BiocGenerics)
x="DataTable", value="ANY"
x="GRangesList", value="ANY"
x="GRangesList", value="character"
x="GenomicRanges", value="ANY"