runDNAcopy(snapCGH)
runDNAcopy()所属R语言包：snapCGH
Results of segmenting an MAList data object using the DNAcopy library
结果分割数据对象MAList使用DNAcopy库
译者：生物统计家园网 机器人LoveR
描述----------Description----------
The results of segmenting data from copy number array experiments from programs such as circular binary segmentation (CBS). This function requires the library DNAcopy to be loaded.
如循环二元分割（CBS）的节目套数阵列实验数据分割的结果。此功能需要库DNAcopy要加载。
用法----------Usage----------
runDNAcopy(input, smooth.region=2, outlier.SD.scale = 4, smooth.SD.scale = 2, trim=0.025, alpha = 0.01, p.method = c("hybrid",
"perm"), kmax = 25, nmin = 200, undo.splits = c("none", "prune", "sdundo"),
undo.prune = 0.05, undo.SD = 3, nperm = 10000, eta = 0.05)
参数----------Arguments----------
参数：input
An object of class MAList or SegList
一个对象类MAList或SegList
参数：smooth.region
number of points to consider on the left and the right of a point to detect it as an outlier.
数点考虑左侧和检测离群点的权利。
参数：outlier.SD.scale
the number of SDs away from the nearest point in the smoothing region to call a point an outlier.
SDS的数量在平滑区域调用一个点离群的最近点距离。
参数：smooth.SD.scale
the number of SDs from the median in the smoothing region where a smoothed point is positioned.
SDS的平滑点定位在平滑区域的中位数。
参数：trim
proportion of data to be trimmed for variance calculation for smoothing outliers and undoing splits based on SD.
方差计算数据的比例进行修整平滑离群撤消分裂的SD。
参数：alpha
significance levels for the test to accept change-points.
接受变点测试的显着水平。
参数：p.method
method used for p-value computation. For the "perm" method the p-value is based on full permutation. For the "hybrid" method the maximum over the entire region is split into maximum of max over small segments and max over the rest. Approximation is used for the larger segment max. Default is hybrid.
P-值计算方法。为“烫发”的方法，p值的基础上充分置换。在整个区域的最大的“混合”的方法分成小部分，并在截断的最大最大最大。用于较大的段最大逼近。默认是混合的。
参数：kmax
the maximum width of smaller segment for permutation in the hybrid method.
较小的混合方法在置换段的最大宽度。
参数：nmin
the minimum length of data for which the approximation of maximum statistic is used under the hybrid method.
下的混合方法使用近似的最大统计数据的最小长度。
参数：undo.splits
A character string specifying how change-points are to be undone, if at all. Default is "none". Other choices are "prune", which uses a sum of squares criterion, and "sdundo", which undoes splits that are not at least this many SDs apart.
一个字符串，指定如何变点被撤消，如果在所有。默认为“无”。其他的选择是“修剪”，它采用了最小二乘准则的总和，的“sdundo”，撤销分裂，是不是至少很多SDS除了。
参数：undo.prune
the proportional increase in sum of squares allowed when eliminating splits if undo.splits="prune".
如果允许时，消除方块的总和的比例增加分裂undo.splits =“剪枝”。
参数：undo.SD
the number of SDs between means to keep a split if undo.splits="sdundo".
之间的SDS意味着保持分裂，如果undo.splits =“sdundo”的。
参数：nperm
number of permutations used for p-value computation.
用于P-值计算的排列数。
参数：eta
the probability to declare a change conditioned on the permuted statistic exceeding the observed statistic exactly j (= 1,...,nperm*alpha) times.
的概率超过观察到的统计准确J（= 1，...，nperm *阿尔法）次置换统计申报条件的变化。
值----------Value----------
The function returns an object of class SegList
该函数返回一个对象类SegList
作者（S）----------Author(s)----------
Mike Smith, based upon DNAcopy help files written by E. S. Venkatraman and Adam Olshen
参见----------See Also----------
segment MAList runHomHMM runGLAD SegList
segmentMAListrunHomHMMrunGLADSegList
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 14:35:37
