peakPloidy(CNAnorm)
peakPloidy()所属R语言包：CNAnorm
Methods for Function peakPloidy in Package ‘CNAnorm’
功能peakPloidy方法包CNAnorm
译者：生物统计家园网 机器人LoveR
描述----------Description----------
peakPloidy Estimate most likely ploidy of genome looking at distribution of smoothed ratio.
peakPloidy估计最有可能的基因套数看着平滑的比例分配。
用法----------Usage----------
## S4 method for signature 'CNAnorm'
peakPloidy(object, method = 'mixture', exclude = character(0),
ploidyToTest = 12, sd = 5, dThresh = 0.01, n = 2048, adjust = .9, force.smooth = TRUE,
reg = FALSE, ds = 1.5, zero.cont = FALSE, ...)
参数----------Arguments----------
参数：object
An object of Class "CNAnorm"
一个对象的类"CNAnorm"
参数：exclude
A character vector with names of Chromosomes/Contigs not to use to estimate ploidy.
特征向量与染色体/重叠群的名称不使用估计套数。
参数：method
A character element matching either "mixture" or "density". Non ambigous partial matches can be used.
字符元素匹配要么"mixture"或"density"。非ambigous部分匹配，可以使用。
参数：ploidyToTest
Maximum ploidy allowed. Warnings! Computation time increases exponentially with this parameter if using "density".
允许的最大套数。警告！如果使用"density"计算时间与此参数成倍增加。
参数：adjust
The "adjust" parameter passed to the density function.
"adjust"参数传递给density功能。
参数：n
The "n" parameter passed to the density function.
"n"参数传递给density功能。
参数：force.smooth
If the input object does not have smoothed ratio, it will smooth using "addSmooth". It is highly recomended to use "force.smooth = TRUE"
如果输入的对象不具有平滑的比例，将顺利使用"addSmooth"。的话，建议使用"force.smooth = TRUE"
参数：sd
Parameter to filter outliers. Values greater than i median + sd * standard deivations will be ignored while detecting peaks and ploidy.
参数过滤离群。我中位数的值大于+ SD *标准deivations检测高峰和套数的同时，都将被忽略。
参数：dThresh
Parameter to filter outliers. Values with a density lower than max(density)*dThresh will be ignored while detecting peaks and ploidy.
参数过滤离群。密度比最大降低值（密度）* dThresh将被忽略，而检测的高峰和套数。
参数：reg
Parameter for mixture model: If set TRUE, the starting point for EM algorithm will be optimized through several methods including regular grid on the ratio distribution. The default is FALSE, by which the starting values are taken from the quantiles of the distribution.
混合模型的参数：如果设置为TRUE，起点为EM算法将通过多种方法，包括定期电网比例分配优化。从分布的分位数，其中初始值默认为FALSE。
参数：ds
Parameter for mixture model: A constraint in EM algorithm of minimum distance between mean estimates, in terms of median standard deviation of the mixture components.
混合模型的参数为：在EM的约束算法的平均估计之间的最小距离，在混合物的组件中位数标准差。
参数：zero.cont
Parameter for mixture model: An argument for the mixture model. If set TRUE, the EM algorithm considers exactly-zero ratios as a mixture component.
混合模型的参数为：混合模型的参数。如果设置为TRUE，EM算法认为，作为一个混合组件的完全零比率。
参数：...
Extra parameters to be passed to funtions for peak detection, specific to each of the methods (deinsity or mixture), se below for details.
通过峰值检测funtions额外的参数，具体到每个方法（deinsity或混合物），硒，详情如下。
值----------Value----------
An object of class "CNAnorm"
一个对象的类"CNAnorm"
注意----------Note----------
Other optional parameters to be passed (...)
其他可选参数传递（...）
mixture method
混合方法
density method
密度法
peakRatioThreshold used to call a peak. Peaks smaller than maxPeakHight/peakRatio are not considered peaks.
peakRatioThreshold用于调用一个高峰。峰比maxPeakHight/peakRatio小峰不考虑。
spacingToleranceA parameter smaller than 1 which describes how strict the program should be on alternative solutions. Only solution with the best R^2 >= max(R^2)*spacingTolerance will be considered as valid.
spacingToleranceA参数小于1，这说明有严格的程序应该是替代方案。唯一的解决方案与最佳R ^ 2> =（，R ^ 2）* spacingTolerance将被视为有效。
interceptRatioMinimum value for the intercept of the linear model. Ideally, should be zero, but the default allows a little flexibility.
线性模型的截距interceptRatioMinimum价值。理想的情况下，应该是零，但默认情况下允许一点点的灵活性。
作者（S）----------Author(s)----------
Stefano Berri <a href="mailto:s.berri@leeds.ac.uk">s.berri@leeds.ac.uk</a> and Arief Gusnanto
<a href="mailto:a.gusnanto@leeds.ac.uk">a.gusnanto@leeds.ac.uk</a>
参考文献----------References----------
(2011) Correcting for cancer genome size and tumour cell content enables better estimation of copy number alterations from next generation sequence
参见----------See Also----------
CNAnorm-class, density
CNAnorm-class，density
举例----------Examples----------
data(LS041)
CN <- dataFrame2object(LS041)
chr2skip <- c("chrY", "chrM")
CN <- gcNorm(CN, exclude = chr2skip)
CN <- addSmooth(CN, lambda = 3)
CN <- peakPloidy(CN, exclude = chr2skip)
# this object CN is what you obtain when you load [此对象的CN是你取得当您载入]
# data(CN)[数据（CN）]
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。
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发表于 2012-2-25 15:37:45
