perWindow(girafe)
perWindow()所属R语言包：girafe
Investigate aligned reads in genome intervals with sliding
调查对齐读取基因间隔滑动
译者：生物统计家园网 机器人LoveR
描述----------Description----------
Investigate aligned reads in genome intervals with sliding windows.
调查对齐读取滑动窗口，在基因组间隔。
用法----------Usage----------
perWindow(object, chr, winsize, step, normaliseByMatches = TRUE,
mem.friendly = FALSE)
参数----------Arguments----------
参数：object
object of class AlignedGenomeIntervals
对象类AlignedGenomeIntervals
参数：chr
string; which chromosome to investigate with sliding windows
字符串;染色体调查与推拉窗
参数：winsize
integer; size of the sliding window in base-pairs
整数;碱基对滑动窗口的大小
参数：step
integer; offset between the start positions of two sliding windows
整数;抵消两个滑动窗口的起始位置之间
参数：normaliseByMatches
logical; should the number of reads per AlignedGenomeInterval be normalised by the number of genomic matches of the read sequence before summing them up in each window? (i.e. derivation a weighted sum of read counts)
逻辑;读取每AlignedGenomeInterval只读序列的基因组比赛标准化之前，他们在每个窗口中总结？ （即派生的读取计数的加权总和）
参数：mem.friendly
logical; argument passed on to function interval_overlap; if TRUE the less RAM and, if the multicore package is attached, multiple processors are used for computing the overlap, on the expense of time
逻辑;参数传递函数interval_overlap如果TRUE较少的RAM，如果multicore包是连接多个处理器用于计算重叠的时间为代价，
Details
详情----------Details----------
The windows are constructed from the first base position onto which a read has been mapped until the end of the chromosome.
窗户从一垒的位置上读取已映射到染色体年底建成。
值----------Value----------
a data.frame with the following information for each sliding window on the chromosome
每个滑动窗口在染色体上的以下信息data.frame
参数：chr
string; which chromosome the interval is on
字符串;染色体区间
参数：start
integer; start coordinate of the windows on the chromosome
整数;开始在染色体上的Windows坐标
参数：end
integer; end coordinate of the windows on the chromosome
整数;窗户在染色体上的结束坐标
参数：n.overlap
integer; number of read match positions inside the window. Per match position there can be one or more reads mapped, so this number always is smaller than n.reads
整数;读匹配的位置，窗口内的数量。每场比赛的位置可以有一个或多个读取映射，所以这个数字始终是小比n.reads
参数：n.reads
numeric; number of reads which match positions inside this window; can be floating-point numbers if argument normaliseByMatches=TRUE
数字;读取数匹配此窗口内的位置，可以是浮点数，如果参数normaliseByMatches=TRUE
参数：n.unique
integer; number of reads which each only have one match position in the genome and for which this position is contained inside this window
整数读取数每次只能有一个匹配的基因组中的位置，这个位置是这个窗口内所载
参数：max.reads
integer; the maximal number of reads at any single one match position contained inside this window
整数;最大读取数在任何一个匹配此窗口内所载的立场
参数：first
integer; coordinate of the first read alignment found inside the window
窗口内发现的第一个读对齐坐标整数;
参数：last
integer; coordinate of the last read alignment found inside the window
窗口内的最后一次读取对齐坐标整数;
The result is of class data.frame and in addition of the (S3) class slidingWindowSummary, which may be utilized by follow-up functions.
结果类data.frame（三）类slidingWindowSummary此外，它可利用的后续功能。
作者（S）----------Author(s)----------
Joern Toedling
参见----------See Also----------
AlignedGenomeIntervals-class
AlignedGenomeIntervals-class
举例----------Examples----------
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")
exPX <- perWindow(exAI, chr="chrX", winsize=1e5, step=0.5e5)
head(exPX[order(exPX$n.overlap, decreasing=TRUE),])
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。
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发表于 2012-2-25 19:52:37
