simulateData(snapCGH)
simulateData()所属R语言包：snapCGH
A function for simulating aCGH data and the corresponding clone layout
一个功能为模拟aCGH数据和相应的克隆布局
译者：生物统计家园网 机器人LoveR
描述----------Description----------
This simulation scheme operates in two stages. Initially, we simulate the layout of clones before using a modified version of the scheme developed by Willenbrock et al., 2005 to generate the \log_2 ratios. For each simulated clone layout we generate 20 sets of simulated \log_2 ratios from one of five templates. Additionally, we also take account of the cellularity of the test sample in our simulation.
这一模拟计划分为两个阶段。最初，我们模拟使用修改后的版本由Willenbrock等，2005年发展计划，以产生\log_2比之前的克隆布局。我们为每个模拟克隆布局的产生了20套模拟\log_2比例从五分之一的模板。此外，我们还利用单元结构的测试样品，在我们的模拟帐户。
用法----------Usage----------
simulateData(nArrays = 20, chrominfo = NULL, prb.short.tiled = 0.5,
prb.long.tiled = 0.5, non.tiled.lower.res = 0.9,
non.tiled.upper.res = 1.1, length.clone.lower = 0.05,
length.clone.upper = 0.2, tiled.lower.res = -0.05,
tiled.upper.res = 0, sd = NULL, output = FALSE,
prb.proportion.tiled = c(0.2, 0.2, 0.2, 0.2, 0.2),
zerolengthnontiled = NULL, zerolengthtiled = NULL,
nonzerolengthnontiled = NULL, nonzerolengthtiled =
NULL, seed = 1)
参数----------Arguments----------
参数：nArrays
The number of arrays we want to simulate
我们要模拟阵列
参数：chrominfo
The information about chromosome length/centromere location to be used. Defaults to the information provided in aCGH package of Jane Fridlyand and Peter Dimitrov.
染色体长度/着丝粒的位置有关的信息被使用。默认aCGH包简Fridlyand和彼得·季米特洛夫提供的信息。
参数：prb.short.tiled
The probability of a tiled region on the short arm of the simulated chromosome (defaults to 0.5).
瓷砖上模拟染色体（默认为0.5）的短臂区域的概率。
参数：prb.long.tiled
The probability of a tiled region on the long arm of the simulated chromosome (defaults to 0.5).
模拟染色体（默认为0.5）的长臂上平铺区域的概率。
参数：non.tiled.lower.res
The lower limit for the distance (in Mbs) between adjacent clones in non-tiled regions of the genome (defaults to 0.9Mb).
的在相邻克隆的基因组（默认到0.9MB）非平铺区域之间的距离（MBS）的下限。
参数：non.tiled.upper.res
The upper limit for the distance (in Mbs) between adjacent clones in non-tiled regions of the genome (defaults to 1.1Mb).
的在相邻克隆的基因组（默认到1.1MB）非平铺区域之间的距离（MBS）的上限。
参数：length.clone.lower
The lower limit for the length (in Mbs) of a clone (this defaults to 0.05Mb).
克隆的长度（MBS）（这默认0.05MB）的下限。
参数：length.clone.upper
The upper limit for the length (in Mbs) of a clone (this defaults to 0.2Mb).
克隆的长度（MBS）（此默认0.2MB）的上限。
参数：tiled.lower.res
The lower limit for the distance (in Mbs) between adjacent clones in tiled regions of the genome (defaults to -0.05Mb).
相邻的克隆基因（默认0.05MB）平铺区域之间的距离（MBS）的下限。
参数：tiled.upper.res
The upper limit for the distance (in Mbs) between adjacent clones in tiled regions of the genome (defaults to 0Mb).
的在相邻克隆的基因组（默认以0MB）平铺区域之间的距离（MBS）的上限。
参数：sd
The standard deviation of the simulated data in each of the states. Defaults to being randomly sampled between 0.1 and 0.2.
在每个州的模拟数据的标准偏差。默认为0.1和0.2之间的随机抽样。
参数：output
A logical variable which is TRUE if you want the output to be written to txt files in the present working directory. Defaults to FALSE.
这是TRUE，如果你想在当前工作目录txt文件被写入输出逻辑变量。默认为false。
参数：prb.proportion.tiled
Given that an arm of a chromosome contains a tiled region this variable (which is a vector of length 5) gives the probability that 20,30,40,50 or 100% of the chromosome is tiled. It defaults to (0.2,0.2,0.2,0.2,0.2)
由于染色体臂包含一个平铺的区域，这个变量（这是一个长度为5的向量）为20,30,40,50或100％的染色体是平铺的概率。它默认为（0.2,0.2,0.2,0.2,0.2）
参数：zerolengthnontiled
The empirical distribution for regions of the genome which are non-tiled and contain no copy number gains or losses. Defaults to zero.length.distr.non.tiled
经验分布的基因组区域，非平铺，并包含没有拷贝数的收益或损失。默认以zero.length.distr.non.tiled
参数：zerolengthtiled
The empirical distribution for regions of the genome which are tiled and contain no copy number gains or losses. Defaults to zero.length.distr.tiled
经验分布区域的基因组是平铺包含没有拷贝数的收益或损失。默认以zero.length.distr.tiled
参数：nonzerolengthnontiled
The empirical distribution for regions of the genome which are non-tiled and contain no copy number gains or losses. Defaults to non.zero.length.distr.non.tiled
经验分布的基因组区域，非平铺，并包含没有拷贝数的收益或损失。默认以non.zero.length.distr.non.tiled
参数：nonzerolengthtiled
The empiricial distribution for regions of the genome which are tiled and contain copy number gains or losses. Defaults to non.zero.length.distr.tiled
empiricial分布区域的基因组是平铺包含拷贝数的收益或损失。默认以non.zero.length.distr.tiled
参数：seed
Seed value allowing simulation to be reproduced if the same seed value is set.
允许转载，如果相同的种子值设置模拟的种子值。
Details
详情----------Details----------
For more details see the article by Marioni and Thorne published in Bioinformatics.
详细内容见由Marioni和Thorne的文章发表在生物信息学。
值----------Value----------
The function returns a list containing the following elements.
该函数返回一个列表，其中包含以下内容。
参数：clones
Gives the start, end and midpoint of the simulated clones.
给出了模拟克隆的起点，终点和中点。
参数：class.output
A list of the true underlying state clones are assigned to for each of the twenty simulations associated with each clone layout.
真正的底层状态的克隆列表被分配到每个克隆布局第二十模拟。
参数：class.matrix
Defines the true underlying state clones are assigned to in each of the five classes
定义真正的底层状态的克隆被分配到五大类，每年
参数：classes
Which of the five class outputs has been used to simulate the \log_2 ratios
五大类输出已用来模拟\log_2比率
参数：datamatrix
A matrix containing twenty columns each of which contains the simulated \log_2 ratios associated with each of the simulations for a particular clone layout.
一个包含20列，其中每个包含模拟\log_2相关比率与每个特定克隆布局模拟的矩阵。
参数：samples
Gives information about the cellularity associated with each of the samples.
给每个样品的单元结构的信息。
作者（S）----------Author(s)----------
John Marioni and Natalie Thorne
参考文献----------References----------
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 14:36:11
