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

loveR

DeCorrelateChannels(Rolexa)
DeCorrelateChannels()所属R语言包：Rolexa

                                        Correct for global correlations and biases
                                         纠正全球的相关性和偏见

                                         译者：生物统计家园网 机器人LoveR

描述----------Description----------

Functions to correct for global correlations between color
功能，以纠正全球的相关性之间的色彩


用法----------Usage----------


## S4 method for signature 'SolexaIntensity'
DeCorrelateChannels(int,cycles=seq(1,dim(int)[3],by=1),theta=matrix(rep(c(0.8806742,1.3727418,0.883865,1.545728),length(cycles)),ncol=4,byrow=TRUE))
## S4 method for signature 'array'
DeCorrelateChannels(int,cycles=seq(1,dim(int)[3],by=1),theta=matrix(rep(c(0.8806742,1.3727418,0.883865,1.545728),length(cycles)),ncol=4,byrow=TRUE))
DeCorrelateChannels(int,...)
## S4 method for signature 'SolexaIntensity'
OptimizeAngle(int,cycles=seq(1,dim(int)[3],by=1),...)
OptimizeAngle(int,...)
## S4 method for signature 'SolexaIntensity'
DeCorrelateCycles(int,ncycles=dim(int)[3],rate=1.8e-2)
## S4 method for signature 'array'
DeCorrelateCycles(int,ncycles=dim(int)[3],rate=1.8e-2)
DeCorrelateCycles(int,...)
## S4 method for signature 'SolexaIntensity'
OptimizeRate(int,ncycles=dim(int)[3],...)
OptimizeRate(int,...)
## S4 method for signature 'RolexaRun'
TileNormalize(run=Rolexa.env,int,cycles=seq(1,dim(int)[3],by=1))
TileNormalize(run,...)



参数----------Arguments----------

参数：run
a RolexaRun object defining the run parameters
RolexaRun对象定义的运行参数


参数：int
a SolexaIntensity object or an array
SolexaIntensity对象或数组


参数：cycles, ncycles
the cycles or the number of cycles (starting from 1) to apply the correction to
周期或周期数（从1开始）申请更正


参数：theta
a length(cycles)*4 matrix with four angles per cycle defining the coordinate changes
length(cycles)*4矩阵定义的坐标变化与每个周期四个角度


参数：rate
the rate of nucleotide mis-incorporation at each cycle
在每个周期率的错误掺入的核苷酸


参数：...
additional arguments passed to optim
额外的参数传递optim


Details

详情----------Details----------

DeCorrelateChannels applies to coordinate transforms: one transforming the axes 1,2 to the axes with angles theta[,1:2] relative to axis 1, and similarly with axes 3,4 and angles theta[,3:4]. These angles can be calculated with OptimizeAngle which minimizes the correlations between channel 1 and 2, and between channel 3 and 4, for each cycle. DeCorrelateCycles assumes that at each cycles, a fraction rate of sequences fail to incorporate any nucleotides and therefore the sequence lengths at each colony display a binomial distribution which is corrected for by taking into account the intensity measured at previous cycles.  OptimizeRate calculates a rate that minimizes correlations between consecutives cycles.
DeCorrelateChannels适用于坐标转换：一是转变角度theta[,1:2]轴1，同样用轴3,4和角度的theta[,3:4]轴1,2轴。这些角度可以计算出OptimizeAngle通道1和2之间的相关性降到最低，通道3和4之间，每个周期。 DeCorrelateCycles假设，在每个周期中，一小部分rate序列未能纳入任何核苷酸，因此序列的长度，在每个殖民地显示，考虑到在先前测量的强度二项分布纠正周期。 OptimizeRate计算速度，最大限度地减少consecutives周期之间的相关性。

TileNormalize estimates the local trend by loess fitting of the model int ~ x+y and substracts it from the intensity matrix.
TileNormalize估计loess拟合的模型int ~ x+y本地的趋势和substracts从强度矩阵。


值----------Value----------

TileNormalize, DeCorrelateChannels and DeCorrelateCycles return an object of the same type as int corrected for spurious correlations. OptimizeAngle returns an length(cycles)*4 matrix and OptimizeRate returns a single positive real
TileNormalize，DeCorrelateChannels和DeCorrelateCyclesint纠正杂散相关的同类型返回一个对象。 OptimizeAngle返回length(cycles)*4矩阵和OptimizeRate返回一个单一的正实


作者（S）----------Author(s)----------


Jacques Rougemont, Arnaud Amzallag, Christian Iseli, Laurent Farinelli, Ioannis Xenarios, Felix Naef



参考文献----------References----------



参见----------See Also----------

TileNormalize
TileNormalize


举例----------Examples----------


path = SolexaPath(system.file("extdata", package="ShortRead"))
rolenv = SetModel(idsep="_")
int = readIntensities(path,pattern="s_1_0001",withVariability=FALSE)

int1 = DeCorrelateChannels(int=int,cycles=1:5,theta=OptimizeAngle(int=int,cycles=1:5))
int2 = DeCorrelateCycles(int=int1,ncycles=5,rate=OptimizeRate(int=int1))
int3 = TileNormalize(run=rolenv,int=int,cycles=1)
seq = CombineReads(run=rolenv,path=path,pattern="s_1_0001_seq*")
PlotCycles(run=rolenv,int=int3,seq=seq,cycles=1:4)

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。