Description Usage Arguments Details Value See Also Examples
Get or set the strand information contained in an object.
1 2 3 4 5 6 7 8 | 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:
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.
1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 | 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"
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