setops-methods(GenomicRanges)
setops-methods()所属R语言包：GenomicRanges
Set operations on GRanges/GRangesList/GappedAlignments objects
设置对农庄/ GRangesList的/ GappedAlignments对象的操作
译者：生物统计家园网 机器人LoveR
描述----------Description----------
Performs set operations on GRanges/GRangesList/GappedAlignments objects.
执行，上农庄/ GRangesList的/ GappedAlignments对象设置操作。
用法----------Usage----------
## Set operations
## S4 method for signature 'GRanges,GRanges'
union(x, y, ignore.strand=FALSE, ...)
## S4 method for signature 'GRanges,GRanges'
intersect(x, y, ignore.strand=FALSE, ...)
## S4 method for signature 'GRanges,GRanges'
setdiff(x, y, ignore.strand=FALSE, ...)
## Parallel set operations
## S4 method for signature 'GRanges,GRanges'
punion(x, y, fill.gap=FALSE, ignore.strand=FALSE, ...)
## S4 method for signature 'GRanges,GRanges'
pintersect(x, y, resolve.empty=c("none", "max.start", "start.x"), ignore.strand=FALSE, ...)
## S4 method for signature 'GappedAlignments,GRanges'
pintersect(x, y, ...)
## S4 method for signature 'GRanges,GRanges'
psetdiff(x, y, ignore.strand=FALSE, ...)
参数----------Arguments----------
参数：x, y
For union, intersect, setdiff, pgap: x and y must both be GRanges objects. For punion: one of x or y must be a GRanges object, the other one can be a GRanges or GRangesList object. For pintersect: one of x or y must be a GRanges object, the other one can be a GRanges, GRangesList or GappedAlignments object. For psetdiff: x and y can be any combination of GRanges and/or GRangesList objects, with the exception that if x is a GRangesList object then y must be a GRangesList too. In addition, for the "parallel" operations, x and y must be of equal length (i.e. length(x) == length(y)).
union，intersect，setdiff，pgap：x和y都必须是农庄的对象。 punion：x或y之一必须是一个农庄对象，其他人可以是一个农庄和GRangesList对象。 pintersect：x或y之一必须是一个农庄对象，其他人可以是一个农庄，GRangesList或GappedAlignments的对象。对于psetdiff：x和y农庄和/或GRangesList的对象可以是任何异常，如果x是GRangesList的对象，那么y结合，必须是一个GRangesList。此外，“水货”的操作，x和y必须是长度相等（即length(x) == length(y)）。
参数：fill.gap
Logical indicating whether or not to force a union by using the rule start = min(start(x), start(y)), end = max(end(x), end(y)).
逻辑表示是否强制使用规则start = min(start(x), start(y)), end = max(end(x), end(y))工会。
参数：resolve.empty
One of "none", "max.start", or "start.x" denoting how to handle ambiguous empty ranges formed by intersections. "none" - throw an error if an ambiguous empty range is formed, "max.start" - associate the maximum start value with any ambiguous empty range, and "start.x" - associate the start value of x with any ambiguous empty range. (See pintersect for the definition of an ambiguous range.)
一"none"，"max.start"或"start.x"表示如何处理模棱两可的路口形成的空范围。 "none" - 抛出一个错误，如果形成一个模糊的范围为空"max.start" - 关联的任何含糊不清的空范围最大的起始值，"start.x" - x关联起始值任何含糊不清的空范围。 （参见pintersect的暧昧范围的定义。）
参数：ignore.strand
For set operations: If set to TRUE, then the strand of x and y is set to "*" prior to any computation. For parallel set operations: If set to TRUE, the strand information is ignored in the computation and the result has the strand information of x.
集合运算：如果设置为TRUE，那么x和y设置为"*"之前任何计算链。对于并行的一套操作：如果设置为TRUE，钢绞线的信息将被忽略在计算结果x链信息。
参数：...
Further arguments to be passed to or from other methods.
进一步的参数被传递或其他方法。
Details
详情----------Details----------
The pintersect methods involving GRanges, GRangesList and/or GappedAlignments objects use the triplet (sequence name, range, strand) to determine the element by element intersection of features, where a strand value of "*" is treated as occurring on both the "+" and "-" strand.
pintersect方法涉及农庄，GRangesList和/或GappedAlignments的对象使用链的价值的"*"被视为元素交汇的特点，来确定该元素的三重（序列的名称，范围，钢绞线） "+"和"-"链发生。
The psetdiff methods involving GRanges and/or GRangesList objects use the triplet (sequence name, range, strand) to determine the element by element set difference of features, where a strand value of "*" is treated as occurring on both the "+" and "-" strand.
psetdiff方法涉及格朗和/或GRangesList的的对象，使用三重（序列的名称，范围，钢绞线）确定元素的元素的功能差集，在股值"*"如发生治疗"+"和"-"链。
值----------Value----------
For union, intersect, setdiff, and pgap: a GRanges.
union，intersect，setdiff，pgap：一个农庄。
For punion and pintersect: when x or y is not a GRanges object, an object of the same class as this non-GRanges object. Otherwise, a GRanges object.
对于punion和pintersect：x或y是不是一个农庄的对象，因为这非农庄对象的相同类的对象。否则，农庄对象。
For psetdiff: either a GRanges object when both x and y are GRanges objects, or a GRangesList object when y is a GRangesList object.
对于psetdiff：要么是农庄的对象，当两个x和y是格朗物体或GRangesList的对象，当y是GRangesList的对象。
作者（S）----------Author(s)----------
P. Aboyoun
参见----------See Also----------
IRanges-setops, GRanges-class, GRangesList-class, GappedAlignments-class, findOverlaps-methods
IRanges-setops，一流的农庄，级GRangesList，GappedAlignments级，findOverlaps方法
举例----------Examples----------
## ---------------------------------------------------------------------[＃------------------------------------------------- --------------------]
## A. SET OPERATIONS[答：＃设置业务]
## ---------------------------------------------------------------------[＃------------------------------------------------- --------------------]
x <- GRanges("chr1", IRanges(c(2, 9) , c(7, 19)), strand=c("+", "-"))
y <- GRanges("chr1", IRanges(5, 10), strand="-")
union(x, y)
union(x, y, ignore.strand=TRUE)
intersect(x, y)
intersect(x, y, ignore.strand=TRUE)
setdiff(x, y)
setdiff(x, y, ignore.strand=TRUE)
## ---------------------------------------------------------------------[＃------------------------------------------------- --------------------]
## B. PARALLEL SET OPERATIONS[＃二平行SET操作]
## ---------------------------------------------------------------------[＃------------------------------------------------- --------------------]
## Not run: [＃无法运行：]
punion(x, shift(x, 7)) # will fail[将失败]
## End(Not run)[＃结束（不运行）]
punion(x, shift(x, 7), fill.gap=TRUE)
pintersect(x, shift(x, 6))
## Not run: [＃无法运行：]
pintersect(x, shift(x, 7)) # will fail[将失败]
## End(Not run)[＃结束（不运行）]
pintersect(x, shift(x, 7), resolve.empty="max.start")
psetdiff(x, shift(x, 7))
## ---------------------------------------------------------------------[＃------------------------------------------------- --------------------]
## C. MORE EXAMPLES[＃C。更多的例子]
## ---------------------------------------------------------------------[＃------------------------------------------------- --------------------]
## GRanges object:[＃农庄对象：]
gr <- GRanges(seqnames=c("chr2", "chr1", "chr1"),
ranges=IRanges(1:3, width = 12),
strand=Rle(strand(c("-", "*", "-"))))
## GRangesList object[＃GRangesList对象]
gr1 <- GRanges(seqnames="chr2",
ranges=IRanges(3, 6))
gr2 <- GRanges(seqnames=c("chr1", "chr1"),
ranges=IRanges(c(7,13), width = 3),
strand=c("+", "-"))
gr3 <- GRanges(seqnames=c("chr1", "chr2"),
ranges=IRanges(c(1, 4), c(3, 9)),
strand=c("-", "-"))
grlist <- GRangesList(gr1=gr1, gr2=gr2, gr3=gr3)
## Parallel intersection of a GRanges and a GRangesList object[＃并行路口1农庄和GRangesList对象]
pintersect(gr, grlist)
pintersect(grlist, gr)
## Parallel intersection of a GappedAlignments and a GRanges object[＃并行路口1 GappedAlignments和农庄对象的]
library(Rsamtools) # because file ex1.bam is in this package[因为文件ex1.bam是在这个包]
galn_file <- system.file("extdata", "ex1.bam", package="Rsamtools")
galn <- readGappedAlignments(galn_file)
pintersect(galn, shift(as(galn, "GRanges"), 6L))
## Parallel set difference of a GRanges and a GRangesList object[＃并行的差集的农庄和1 GRangesList对象]
psetdiff(gr, grlist)
## Parallel set difference of two GRangesList objects[＃并行差集两个GRangesList对象的]
psetdiff(grlist, shift(grlist, 3))
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注：
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发表于 2012-2-25 19:29:57
