Description Usage Arguments Details Value Author(s) See Also Examples

A bunch of useful `strand`

and `invertStrand`

methods.

1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 | ```
## S4 method for signature 'missing'
strand(x)
## S4 method for signature 'character'
strand(x)
## S4 method for signature 'factor'
strand(x)
## S4 method for signature 'integer'
strand(x)
## S4 method for signature 'logical'
strand(x)
## S4 method for signature 'Rle'
strand(x)
## S4 method for signature 'RleList'
strand(x)
## S4 method for signature 'DataTable'
strand(x)
## S4 replacement method for signature 'DataTable,ANY'
strand(x) <- value
## S4 method for signature 'character'
invertStrand(x)
## S4 method for signature 'factor'
invertStrand(x)
## S4 method for signature 'integer'
invertStrand(x)
## S4 method for signature 'logical'
invertStrand(x)
## S4 method for signature 'Rle'
invertStrand(x)
## S4 method for signature 'RleList'
invertStrand(x)
``` |

`x` |
The object from which to obtain a |

`value` |
Replacement value for the strand. |

All the `strand`

and `invertStrand`

methods documented
here return either a *strand factor*, *strand factor
Rle*, or *strand factor RleList* object.
These are factor, factor-Rle, or factor-RleList
objects containing the "standard strand levels" (i.e. `+`

, `-`

,
and `*`

) and no NAs.

All the `strand`

and `invertStrand`

methods documented here
return an object that is *parallel* to input object `x`

when
`x`

is a character, factor, integer, logical, Rle,
or RleList object.

For the `strand`

methods:

If

`x`

is missing, returns an empty factor with the "standard strand levels" i.e.`+`

,`-`

, and`*`

.If

`x`

is a character vector or factor, it is coerced to a factor with the levels listed above.`NA`

values in`x`

are not accepted.If

`x`

is an integer vector, it is coerced to a factor with the levels listed above.`1`

,`-1`

, and`NA`

values in`x`

are mapped to the`+`

,`-`

, and`*`

levels respectively.If

`x`

is a logical vector, it is coerced to a factor with the levels listed above.`FALSE`

,`TRUE`

, and`NA`

values in`x`

are mapped to the`+`

,`-`

, and`*`

levels respectively.If

`x`

is a character-, factor-, integer-, or logical-Rle, it is transformed with`runValue(x) <- strand(runValue(x))`

and returned.If

`x`

is an RleList object, each list element in`x`

is transformed by calling`strand()`

on it and the resulting RleList object is returned. More precisely the returned object is`endoapply(x, strand)`

. Note that in addition to being*parallel*to`x`

, this object also has the same*shape*as`x`

(i.e. its list elements have the same lengths as in`x`

).If

`x`

inherits from`DataTable`

, the`"strand"`

column is passed thru`strand()`

and returned. If`x`

has no`"strand"`

column, this return value is populated with`*`

s.

Each `invertStrand`

method returns the same object as its corresponding
`strand`

method but with `"+"`

and `"-"`

switched.

M. Lawrence and H. Pag<c3><a8>s

1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40 41 42 | ```
strand()
x1 <- c("-", "*", "*", "+", "-", "*")
x2 <- factor(c("-", "-", "+", "-"))
x3 <- c(-1L, NA, NA, 1L, -1L, NA)
x4 <- c(TRUE, NA, NA, FALSE, TRUE, NA)
strand(x1)
invertStrand(x1)
strand(x2)
invertStrand(x2)
strand(x3)
invertStrand(x3)
strand(x4)
invertStrand(x4)
strand(Rle(x1))
invertStrand(Rle(x1))
strand(Rle(x2))
invertStrand(Rle(x2))
strand(Rle(x3))
invertStrand(Rle(x3))
strand(Rle(x4))
invertStrand(Rle(x4))
x5 <- RleList(x1, character(0), as.character(x2))
strand(x5)
invertStrand(x5)
strand(DataFrame(score=2:-3))
strand(DataFrame(score=2:-3, strand=x3))
strand(DataFrame(score=2:-3, strand=Rle(x3)))
## Sanity checks:
target <- strand(x1)
stopifnot(identical(target, strand(x3)))
stopifnot(identical(target, strand(x4)))
stopifnot(identical(Rle(strand(x1)), strand(Rle(x1))))
stopifnot(identical(Rle(strand(x2)), strand(Rle(x2))))
stopifnot(identical(Rle(strand(x3)), strand(Rle(x3))))
stopifnot(identical(Rle(strand(x4)), strand(Rle(x4))))
``` |

LiNk-NY/GenomicRanges documentation built on May 9, 2017, 5:14 a.m.

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