mappabilityCalc(Repitools)
mappabilityCalc()所属R语言包：Repitools
Calculate The Mappability of a Region
计算一个区域的Mappability
译者：生物统计家园网 机器人LoveR
描述----------Description----------
Function to calculate mappability of windows
函数来计算的Windows mappability
用法----------Usage----------
## S4 method for signature 'GRanges'
mappabilityCalc(x, organism, window = NULL,
type = c("block", "TSS", "center"), verbose = TRUE)
## S4 method for signature 'data.frame'
mappabilityCalc(x, organism, window = NULL,
type = c("block", "TSS", "center"), ...)
参数----------Arguments----------
参数：x
A GRanges object or a data.frame, with columns chr and either position or start, end and strand.
一个GRanges对象或data.frame列chr或者position或start，end和strand。
参数：window
Bases around the locations that are in the window. Calculation will consider windowSize/2 bases upstream, and windowSize/2-1 bases downstream. </table>
窗口的位置，在碱基周围。计算将考虑windowSize/2上游碱基，windowSize/2-1碱基下游。 </ TABLE>
参数：type
What part of the interval to make the window around. If the value is "TSS", the the start coordinate is used for all + strand features, and the end coordinate is used for all - strand features. If "cemter" is chosen, then the coordinate that is half way between the start and end of each feature will be used as the reference point. "block" results in the use the start and end coordinates without modification.
哪一部分的时间间隔，使周围的窗口。如果该值是"TSS"，起始坐标是用来为所有+链的特点，和结束坐标用于所有 - 链功能。 "cemter"如果选择，然后坐标是成功的一半各功能之间的开始和结束的方式将被用来作为参考点。 "block"结果在使用未经修改的起点和终点坐标。
参数：organism
The BSgenome object to calculate mappability upon.
BSgenome对象计算mappability后。
参数：verbose
Whether to print the progess of processing.
无论是打印处理陆侃。
参数：...
The verbose variable for the data.frame method, passed onto the GRanges method.
verbosedata.frame方法通过GRanges方法上，变量。
Details
详情----------Details----------
The windows considered will be windowSize/2 bases upstream and windowSize/2-1 bases downstream of the given position of stranded features, and the same number of bases towards the start and end of the chromosome for unstranded features. The value returned for each region is a percentage of bases in that region that are not N (any base in IUPAC nomenclature).
窗户考虑将windowSize/2立足上游和windowSize/2-1碱基下游的搁浅功能的位置，相同数量的碱基对的开始和结束unstranded功能的染色体。为每个区域的返回值是在该区域的碱基，是不是n（任何IUPAC命名法的基础）的百分比。
For any positions of a window that are off the end of a chromosome, they will be considered as being N.
染色体年底关闭一个窗口的任何位置，他们将被视为是北
值----------Value----------
A vector of mappability percentages, one for each region.
一个向量mappability百分比，每个区域之一。
作者（S）----------Author(s)----------
Aaron Statham
举例----------Examples----------
## Not run: [＃无法运行：]
require(BSgenome.Hsapiens36bp.UCSC.hg18mappability)
TSSTable <- data.frame(chr = paste("chr", c(1,2), sep = ""), position = c(100000, 200000))
mappabilityCalc(TSSTable, Hsapiens36bp, window = 200, type = "TSS")
## End(Not run)[＃结束（不运行）]
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 12:51:09
