estProfileWithMBPCRforOligoSnpSet(mBPCR)
estProfileWithMBPCRforOligoSnpSet()所属R语言包：mBPCR
Estimate and print the copy number profile of some chromosomes of samples in an oligoSnpSet object
估计和打印样品一些染色体的拷贝数剖面在oligoSnpSet对象
译者：生物统计家园网 机器人LoveR
描述----------Description----------
Function to estimate the copy number profile with a piecewise constant function using mBPCR. Eventually, it is possible to estimate the profile with a smoothing curve, using either the Bayesian Regression Curve with K_2 (BRC with K_2) or the Bayesian Regression Curve Averaging over k (BRCAk). It is also possible to choose the estimator of the variance of the levels rhoSquare (i.e. either \hat{ρ}_1^2 or \hat{ρ}^2) and by default \hat{ρ}_1^2 is used.
函数来估计与分段常数使用mBPCR功能的拷贝数配置文件。最终，它是可能的，估计与平滑的曲线轮廓，使用贝叶斯回归曲线与K_2（商业登记证与K_2）或贝叶斯回归曲线，平均超过K（BRCAk）。它也可以选择水平的方差估计rhoSquare（即：要么\hat{ρ}_1^2或\hat{ρ}^2）和默认的\hat{ρ}_1^2使用。
用法----------Usage----------
estProfileWithMBPCRforOligoSnpSet(sampleData, sampleToBeAnalyzed, chrToBeAnalyzed, maxProbeNumber, ifLogRatio=1,
rhoSquare=NULL, kMax=50, nu=NULL, sigmaSquare=NULL, typeEstRho=1, regr=NULL)
参数----------Arguments----------
参数：sampleData
object of type oligoSnpSet. The following fields must not be empty: assayData(sampleData)$copyNumber (it contains the raw copy number values), featureNames(featureData(sampleData)) (it contains the names of the SNPs), featureData(sampleData)$chromosome (it contains the names of the chromosomes to which each of the SNPs belongs), featureData(sampleData)$position (it contains the physical positions of the SNPs).
对象类型oligoSnpSet。以下字段不能为空：assayData(sampleData)$copyNumber（它包含了原始的拷贝数值），featureNames(featureData(sampleData))（它包含的SNPs的名字），featureData(sampleData)$chromosome（它包含名称染色体的SNP属于），featureData(sampleData)$position（包含物理位置的SNP）。
参数：sampleToBeAnalyzed
vector containing the number of the columns corresponding to the samples the user wants to analyze.
向量列相应的用户要分析的样品数量。
参数：chrToBeAnalyzed
array containing the name of the chromosomes that the user wants to analyze. The possible values of the chromosomes are: the integers from 1 to 22, 'X' and 'Y'.
数组，包含染色体的名称，用户要分析。染色体可能的值是：从1到22的整数，“X”和“Y”。
参数：maxProbeNumber
maximum number of probes that a chromosome (or arm of a chromosome) can have to be analyzed. The procedure of profile estimation needs the computation of an array of length (length(chromosome)+1)*(length(chromosome)+2)/2. To be sure to have set this parameter correctly, try to create the array A <- array(1, dim=(maxProbeNumber+1)*(maxProbeNumber+2)/2), before starting with the estimation procedure.
探针染色体（或染色体臂）进行分析的最大数量。个人资料估计的过程，需要计算数组的长度(length(chromosome)+1)*(length(chromosome)+2)/2。要确保已正确设置此参数，尝试创建数组A <- array(1, dim=(maxProbeNumber+1)*(maxProbeNumber+2)/2)之前，估计程序的开始。
参数：ifLogRatio
denotes if the data are either the log2ratio of raw copy number data or raw copy number data. By default, they are considered as log2ratio data, otherwise (ifLogRatio=0) they are transformed in log2ratio data.
表示，如果数据是原始拷贝数的数据或原始拷贝数数据log2ratio。默认情况下，他们被视为log2ratio数据，否则（ifLogRatio=0）他们在log2ratio数据转化。
参数：rhoSquare
variance of the segment levels. If rhoSquare=NULL, then the algorithm estimates it on the sample.
段水平的差异。如果rhoSquare=NULL，然后算法估计样品。
参数：kMax
maximum number of segments
段的最大数量
参数：nu
mean of the segment levels. If nu=NULL, then the algorithm estimates it on the sample.
指段的水平。如果nu=NULL，然后算法估计样品。
参数：sigmaSquare
variance of the noise. If sigmaSquare=NULL, then the algorithm estimates it on the sample.
噪声方差。如果sigmaSquare=NULL，然后算法估计样品。
参数：typeEstRho
choice of the estimator of rhoSquare. If typeEstRho=1, then the algorithm estimates rhoSquare with \hat{ρ}_1^2, while if typeEstRho=0, it estimates rhoSquare with \hat{ρ}^2.
rhoSquare估计的选择。如果typeEstRho=1，然后算法估计rhoSquare用\hat{ρ}_1^2，而typeEstRho=0如果，估计rhoSquare\hat{ρ}^2。
参数：regr
choice of the computation of the regression curve. If regr=NULL, then the regression curve is not computed, if regr="BRC" the Bayesian Regression Curve is computed (BRC with K_2), if regr="BRCAk" the Bayesian Regression Curve Averaging over k is computed (BRCAk).
计算回归曲线的选择。如果regr=NULL，然后回归曲线没有计算，如果regr="BRC"贝叶斯回归曲线计算（商业登记证与K_2），如果regr="BRCAk"贝叶斯回归曲线，平均在K计算机（BRCAk）。
Details
详情----------Details----------
By default, the function estimates the copy number profile with mBPCR and estimating rhoSquare on the sample, using \hat{ρ}_1^2. It is also possible to use \hat{ρ}^2 as estimator of rhoSquare, by setting typeEstRho=0, or to directly set the value of the parameter.
默认情况下，功能估计与mBPCR副本数量的个人资料和样品rhoSquare估计，使用\hat{ρ}_1^2。它也可以使用\hat{ρ}^2估计rhoSquare，通过设置typeEstRho=0，或直接设置的参数值。
The function gives also the possibility to estimate the profile with a Bayesian regression curve: if regr="BRC" the Bayesian Regression Curve with K_2 is computed (BRC with K_2), if regr="BRCAk" the Bayesian Regression Curve Averaging over k is computed (BRCAk).
该功能也给的可能性估计与贝叶斯回归曲线轮廓：如果regr="BRC"K_2贝叶斯回归曲线是计算机，如果K_2（regr="BRCAk"，BRC）贝叶斯回归曲线，平均在K计算机（BRCAk）。
值----------Value----------
A list containing:
一份列表，列出：
参数：estPC
an oligoSnpSet equal to sampleData apart from the field assayData(estPC)$copyNumber, which contains the estimated profile with mBPCR
oligoSnpSet平等的sampleData除了从外地assayData(estPC)$copyNumber，其中包含与mBPCR的估计轮廓
参数：regrCurve
an oligoSnpSet equal to sampleData apart from the field assayData(regrCurve)$copyNumber, which contains the estimated bayesian regression curve. This object is returned only if regr!=NULL.
oligoSnpSet平等的sampleData除了从外地assayData(regrCurve)$copyNumber，其中包含的估计贝叶斯回归曲线。返回此对象只有regr!=NULL。
The matrices assayData(estPC)$copyNumber and assayData(regrCurve)$copyNumber have the same dimension of assayData(sampleData)$copyNumber, hence their elements, corresponding to the not analyzed chromosomes and samples, are equal to NA.
矩阵assayData(estPC)$copyNumber和assayData(regrCurve)$copyNumber的assayData(sampleData)$copyNumber同一维度，因此它们的元素，没有分析的染色体和样品对应，等于NA的。
参考文献----------References----------
Bayesian DNA copy number analysis. BMC Bioinformatics 10: 10. http://www.idsia.ch/~paola/mBPCR
参见----------See Also----------
estProfileWithMBPCR, computeMBPCR
estProfileWithMBPCR，computeMBPCR
举例----------Examples----------
###import an example of oligoSnpSet data[＃＃导入oligoSnpSet数据的例子]
#data(sample.snpset)[数据（sample.snpset）]
##estimation of chromosome 1 in sample 3 [＃估计在1号染色体样本3]
#r <- estProfileWithMBPCRforOligoSnpSet(sample.snpset, sampleToBeAnalyzed=3, chrToBeAnalyzed=1, maxProbeNumber=1000, ifLogRatio=0, rhoSquare= 0.0889637)[R < - estProfileWithMBPCRforOligoSnpSet（sample.snpset，sampleToBeAnalyzed = 3，chrToBeAnalyzed = 1，maxProbeNumber = 1000，ifLogRatio = 0，rhoSquare = 0.0889637）]
##plot of the estimated chromosomes[＃预计染色体积]
#cc <- r$estPC[CC < - R $ estPC]
#cc1 <- cc[chromosome(cc) == "1",3][CC1 < - CC染色体（CC）==“1”，3]]
#graph.par <- plotSnp(cc1)[graph.par < - plotSnp（CC1）]
#graph.par$ylim <- c(-0.23, 0.1)[graph.par ylim元< - C（-0.23，0.1）]
#graph.par$cytoband.ycoords <- c(-0.22, -0.18)[graph.par | $ cytoband.ycoords < - C（-0.22，-0.18）]
#print(graph.par)[打印（graph.par）]
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。
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发表于 2012-2-26 00:33:33
