which_nearest-methods(girafe)
which_nearest-methods()所属R语言包：girafe
Methods for function 'which_nearest' and genome intervals
函数which_nearest“和基因间隔方法
译者：生物统计家园网 机器人LoveR
描述----------Description----------
For each genome interval in one set, finds the nearest interval in a second set of genome intervals.
对于每个集于一体的基因组区间，发现最近在第二组的基因组间隔的时间间隔。
值----------Value----------
a data.frame with a number of rows equal to the number of intervals in argument from. The elements of the data.frame are:
data.frame行相等的时间间隔参数from。数据框元素是：
参数：distance_to_nearest
numeric; distance to nearest interval from object to. Is 0 if the current interval in object from did overlap one or more intervals in object to
数字对象to最近的间隔距离。如果在当前间隔对象from没有重叠在一个或多个对象to间隔是0
参数：which_nearest
list; each list element are the indices or the intervals in object to that have the closest distance to the current interval in object from
列表，每个列表元素，有最近距离的对象到当前的时间间隔to指数或在对象from间隔
参数：which_overlap
list; each list element are the indices or the intervals in object to that do overlap with the current interval in object from
列表，每个列表元素to，当前间隔重叠对象from指数或对象的时间间隔
方法----------Methods----------
Currently, the package girafe contains method implementations for the first object (Argument: from) being of any of the classes “AlignedGenomeIntervals”,“Genome_intervals” or “Genome_intervals_stranded”. The second object (Argument: to) has be of class “Genome_intervals_stranded” or “Genome_intervals”.
目前，的包girafe包含的第一个对象的方法实现（参数：from）的任何类的“AlignedGenomeIntervals”，“Genome_intervals”或“Genome_intervals_stranded”。第二个对象（参数：to）已成为的的“Genome_intervals_stranded”类或“Genome_intervals”。
注意----------Note----------
If the supplied objects are stranded, as it is the case with objects of classes "AlignedGenomeIntervals" and "Genome_intervals_stranded", then the overlap and distance is solely computed between intervals on the same strand.
如果所提供的对象被搁浅，因为它是对象类的AlignedGenomeIntervals“和Genome_intervals_stranded”，然后重叠和距离的情况下，仅计算在同一链之间的间隔。
For objects of class "Genome_intervals", overlap and distances are computed regardless of strand information.
重叠和距离对于类的Genome_intervals“的对象，无论是计算链的信息。
作者（S）----------Author(s)----------
Joern Toedling
参见----------See Also----------
which_nearest
which_nearest
举例----------Examples----------
### process aligned reads[＃处理对齐读取]
exDir <- system.file("extdata", package="girafe")
exA <- readAligned(dirPath=exDir, type="Bowtie",
pattern="aravinSRNA_23_no_adapter_excerpt_mm9_unmasked.bwtmap")
exAI <- as(exA, "AlignedGenomeIntervals")
## load annotated genome features[＃加载注释的基因组功能]
load(file.path(exDir, "mgi_gi.RData"))
## subset for sake of speed:[＃子集，为了速度：]
A <- exAI[is.element(seq_name(exAI), c("chrX","chrY"))]
G <- mgi.gi[is.element(seq_name(mgi.gi), c("chrX","chrY"))]
## find nearest annotated feature for each AlignedGenomeInterval[＃发现最近每个AlignedGenomeInterval注释功能]
WN <- which_nearest(A, G)
dim(WN); tail(WN)
## notice the difference to:[＃注意到其中的差别：]
tail(which_nearest(as(A, "Genome_intervals"), G))
# the last interval in A is located antisense to a gene,[在最后一个区间位于一个基因的反义，]
# but not overlapping anything on the same strand[但不重叠的相同链上的任何东西]
转载请注明:出自 生物统计家园网(http://www.biostatistic.net)。
注：
注1：为了方便大家学习，本文档为生物统计家园网机器人LoveR翻译而成，仅供个人R语言学习参考使用，生物统计家园保留版权。
注2：由于是机器人自动翻译，难免有不准确之处，使用时仔细对照中、英文内容进行反复理解，可以帮助R语言的学习。
注3：如遇到不准确之处，请在本贴的后面进行回帖，我们会逐渐进行修订。
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发表于 2012-2-25 19:58:49
