R语言 GenomicRanges包 utils()函数中文帮助文档(中英文对照)

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utils(GenomicRanges)
utils()所属R语言包：GenomicRanges

                                         seqlevels utility functions
                                         seqlevels实用功能

                                         译者：生物统计家园网 机器人LoveR

描述----------Description----------

Rename or subset the seqlevels in a GenomicRanges, GRangesList  or GappedAlignments object.
重命名或子集，在GenomicRanges，GRangesList或GappedAlignments对象seqlevels。


用法----------Usage----------


  ## S4 method for signature 'GenomicRanges,GenomicRanges'
keepSeqlevels(x, value, ...)
  ## S4 method for signature 'GenomicRanges,GRangesList'
keepSeqlevels(x, value, ...)
  ## S4 method for signature 'GenomicRanges,GappedAlignments'
keepSeqlevels(x, value, ...)
  ## S4 method for signature 'GenomicRanges,character'
keepSeqlevels(x, value, ...)
  ## S4 method for signature 'GRangesList,GenomicRanges'
keepSeqlevels(x, value, ...)
  ## S4 method for signature 'GRangesList,GRangesList'
keepSeqlevels(x, value, ...)
  ## S4 method for signature 'GRangesList,GappedAlignments'
keepSeqlevels(x, value, ...)
  ## S4 method for signature 'GRangesList,character'
keepSeqlevels(x, value, ...)
  ## S4 method for signature 'GappedAlignments,GenomicRanges'
keepSeqlevels(x, value, ...)
  ## S4 method for signature 'GappedAlignments,GRangesList'
keepSeqlevels(x, value, ...)
  ## S4 method for signature 'GappedAlignments,GappedAlignments'
keepSeqlevels(x, value, ...)
  ## S4 method for signature 'GappedAlignments,character'
keepSeqlevels(x, value, ...)

  ## S4 method for signature 'GenomicRanges,character'
renameSeqlevels(x, value, ...)
  ## S4 method for signature 'GRangesList,character'
renameSeqlevels(x, value, ...)
  ## S4 method for signature 'GappedAlignments,character'
renameSeqlevels(x, value, ...)



参数----------Arguments----------

参数：x
The GenomicRanges, GRangesList or GappedAlignments object  for which the seqlevels will be removed or renamed.  
在GenomicRanges，GRangesList或GappedAlignments对象的seqlevels将被删除或改名。


参数：value
For keepSeqlevels, a GRanges, GRangesList or GappedAlignments or character vector. The seqlevels from  value object will be used to subset the seqlevels in the x.   For renameSeqlevels, a named character vector where the names are the  'old' seqlevels and the values are the 'new' seqlevels. seqlevels in  the x will be renamed from the 'old' to the 'new'.   
keepSeqlevels，农庄，GRangesList或GappedAlignments或特征向量。将用于子集valueseqlevels从x对象seqlevels。 renameSeqlevels，一个名为特征向量的名称是老seqlevels和价值观是新seqlevels。 x seqlevels将改名为老的新。


参数：...
Arguments passed to other functions.  
参数传递等功能。


Details

详情----------Details----------

Many operations on GRanges objects require the seqlevels  to match before a comparison can be made  (e.g., findOverlaps(type="within")). keepSeqlevels and renameSeqlevels are convenience functions  for subsetting and renaming the seqlevels of these objects.
农庄对象的许多操作要求seqlevels匹配之前，可以比较（例如，findOverlaps(type="within")）。 keepSeqlevels和renameSeqlevels子集，并重新命名这些对象的seqlevels方便的功能。

The keepSeqlevels function subsets the seqlevels of x  based on the seqlevels provided in value. seqlevels contained in value that are not in x are ignored. If none of the seqlevels in the value are present in x an error is thrown.  When x is a GRangesList, keepSeqlevels retains only the seqlevels specified in value. If a list element has multiple chromosomes but not all chromosomes are specified in value, a reduced list element is returned. All empty list elements are dropped. See examples.
keepSeqlevels功能子集的seqlevelsx上根据value提供的seqlevels。 seqlevels所载value是x被忽略。如果没有seqlevelsvalue是目前x抛出一个错误。当x是一个GRangesList，keepSeqlevels保留只有在value指定seqlevels。如果列表中的元素有多个染色体，但并不是所有的染色体在value指定，减少列表中的元素被返回。所有空列表中的元素都将被丢弃。看到的例子。

renameSeqlevels renames the seqlevels in x based on those provided in value. value is a named character vector where the names should match existing seqlevels in x. The matching seqlevels will be renamed to the corresponding list values. List names in value that are not in  x are ignored. An error is thrown if none of the list names in  value match the seqlevels in x
renameSeqlevels重命名的seqlevelsx在value提供的基础。 value是一个命名的特征向量的名称应符合现有seqlevelsx。的的匹配seqlevels将被重新命名为相应的列表值。列表名称value不x被忽略。抛出一个错误，如果没有在valuex匹配seqlevels列表名称


值----------Value----------

The x object with seqlevels removed or renamed.
x对象seqlevels删除或改名。


作者（S）----------Author(s)----------


Valerie Obenchain <a href="mailto:vobencha@fhcrc.org">vobencha@fhcrc.org</a>



举例----------Examples----------



gr1 <- GRanges(seqnames = c("chr1", "chr2"),
          ranges = IRanges(c(7,13), width = 3),
          strand = c("+", "-"), score = 3:4, GC = c(0.3, 0.5))
gr2 <- GRanges(seqnames = c("chr1", "chr1", "chr2", "chr3", "chr3"),
          ranges = IRanges(c(1, 4, 8, 9, 16), width=5),
          strand = "-", score = c(3L, 2L, 5L, 6L, 2L),
          GC = c(0.4, 0.1, 0.55, 0.20, 0.10))
gr3 <- GRanges(seqnames = c("CHROM4", "CHROM4"),
               ranges = IRanges(c(20, 45), width=6),
               strand = "+", score = c(2L, 5L), GC = c(0.30, 0.45))

## GRanges :[＃农庄：]
gr3_rename <- renameSeqlevels(gr3, c(CHROM4="chr4"))
gr3_rename

gr2_subset_chr <- keepSeqlevels(gr2, c("chr1", "chr2"))
gr2_subset_gr <- keepSeqlevels(gr2, gr1)
identical(gr2_subset_chr, gr2_subset_gr)

## GRangesList :[＃GRangesList：]
grl1 <- GRangesList("gr1" = gr1, "gr2" = gr2, "gr3" = gr3)
grl2 <- GRangesList("gr1" = gr1, "gr2" = gr2, "gr3" = gr3_rename)
grl1_rename <- renameSeqlevels(grl1, c(CHROM4="chr4"))
identical(grl1_rename, grl2)

grl1_subset <- keepSeqlevels(grl1, "chr3")

## GappedAlignments :[＃GappedAlignments：]
library(Rsamtools)
galn_file <- system.file("extdata", "ex1.bam", package="Rsamtools")
galn <- readGappedAlignments(galn_file)

galn_rename <- renameSeqlevels(galn, c(seq2="chr2"))
galn_subset <- keepSeqlevels(galn_rename, gr1)
galn_subset

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