cpgDensityCalc(Repitools)
cpgDensityCalc()所属R语言包：Repitools
Calculate CpG Density in a Window
在一个窗口计算的CpG密度
译者：生物统计家园网 机器人LoveR
描述----------Description----------
Function to calculate CpG density around a position.
函数来计算的CpG密度周围的位置。
用法----------Usage----------
## S4 method for signature 'data.frame,BSgenome'
cpgDensityCalc(x, organism, ...)
## S4 method for signature 'GRangesList,BSgenome'
cpgDensityCalc(x, organism, verbose = TRUE, ...)
## S4 method for signature 'GRanges,BSgenome'
cpgDensityCalc(x, organism, seq.len = NULL, window = NULL,
w.function = c("none", "linear", "exp", "log"),
verbose = TRUE)
参数----------Arguments----------
参数：x
A data.frame, with columns chr and position, or columns chr, start, end, and strand. Also may be a GRangesList object, or GRanges.
一个data.frame，列chr和position，或列chr，start，end，strand。也可能是一个GRangesList对象，或GRanges。
参数：window
Bases around the locations that are in the window. Calculation will consider window/2 - 1 bases upstream, and window/2 bases downstream.
窗口的位置，在碱基周围。计算将考虑window/2 - 1上游碱基，window/2碱基下游。
参数：w.function
Weighting function to use. Can be "none", "linear", "log", or "exp"
加权函数的使用。可以"none"，"linear"，"log"或"exp"
参数：organism
The BSgenome object to calculate CpG density upon.
BSgenome对象计算的CpG密度后。
参数：seq.len
The fragment size of the sequence reads in x. Default: No extension.
该序列的片段大小读取x。默认：无扩展。
参数：verbose
Print details of processing.
打印处理的细节。
参数：...
Arguments passed into the data.frame or GRangesList method, but not used until the GRanges method.
data.frame或GRangesList方法，但直到GRanges方法不使用参数传递。
Details
详情----------Details----------
If the version of the data frame with the start, end, and strand columns is given, the window will be created around the TSS.
如果给出的数据框的起点，终点和钢绞线列的版本，将创建的窗口周围的TSS。
For weighting scheme "none", this is equivalent to the number of CG matches in the region. For "linear" weighting, each match is given a score 1/x where x is the number of bases from the postition that the match occurred, and the scores are summed. For exponential weighting and logarithmic weighting, the idea is similar, but the scores decay exponentially (exp^-5x/window) and logarithmically (log2(2 - (distancesForRegion / window))).
加权计划"none"，这相当于在该区域的CG比赛。 "linear"比重，每场比赛得分1/x其中x是从的postition比赛发生的碱基数量，分数相加。加权指数和对数加权，这个想法是相似的，但分数指数衰减（exp^-5x/window）和对数（log2(2 - (distancesForRegion / window))）。
值----------Value----------
A numeric vector of CpG densities for each region.
一个numeric为每个区域的CpG密度矢量。
作者（S）----------Author(s)----------
Dario Strbenac
举例----------Examples----------
if(require(BSgenome.Hsapiens.UCSC.hg18))
{
TSSTable <- data.frame(chr = c("chr1", "chr2"), position = c(100000, 200000))
cpgDensityCalc(TSSTable, organism = Hsapiens, window = 600)
}
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 2012-2-26 12:48:53
