LOHclonality(Clonality)
LOHclonality()所属R语言包：Clonality
Clonality testing using LOH (Loss of Heterozygosity) profiles
克隆试验使用蕙（杂合性丢失）型材
译者：生物统计家园网 机器人LoveR
描述----------Description----------
Function to test clonality of two tumors from the same patient based on their LOH profiles. This function implements Concordant Mutations and Likelihood Ratio tests.
功能测试两个肿瘤克隆从蕙型材基于相同的病人。此功能实现的谐和突变和似然比检验。
用法----------Usage----------
LOHclonality(LOHtable, ptlist, refLOHtable = NULL, pfreq = NULL, noloh, loh1, loh2,method="both")
参数----------Arguments----------
参数：LOHtable
Matrix of LOH calls. Each row corresponds to a marker. First column contains the names of the markers. Each other column represents a sample and contains LOH calls.
矩阵蕙检测。每一行对应一个标记。第一列包含标记的名称。每一列代表一个样本，并包含蕙检测。
参数：ptlist
Vector of the patient IDs in the order the samples appear in the data. For example, if the first three tumors (columns 3, 4, 5 of data) belong to patient A, and the following two (columns 6, 7 of data) belong to patient B, then ptlist=c('ptA', 'ptA', 'ptA', 'ptB', 'ptB').
患者ID的顺序向量的样本中出现的数据。例如，如果前三肿瘤（列3，4，5）的数据属于病人，以下两种（6，7的数据列）属于患者B，然后ptlist = C（“PTA”，“角，角，肺结核，PTB）。
参数：refLOHtable
Matrix of LOH calls that should be used to calculate the LOH frequencies used in Likelihood Ration calculation. The structure is similar to LOHtable. If refLOHtable is not specified, frequencies are calcualted from LOHtable.
矩阵蕙呼吁，应该用来计算蕙似然定额计算中使用的频率。结构类似LOHtable。如果未指定refLOHtable，频率从LOHtable calcualted。
参数：pfreq
Vector of LOH frequencies known from the literature. Should be in the same order as the markers in LOHtable. If pfreq is not specified, frequencies are calcualted from LOHtable.
从文献中被称为蕙频率的向量。应该是在作为标记LOHtable的顺序相同。如果未指定pfreq，频率从LOHtable calcualted。
参数：noloh
The string or a number that denotes absence of LOH.
字符串或一个数字表示蕙缺席的。
参数：loh1
The string or a number that denotes presence of LOH.
字符串或数字表示蕙存在的。
参数：loh2
The string or a number that denotes presence of LOH that is discordant from loh1.
字符串或一个数字，表示的LOH的存在是从loh1的不和谐。
参数：method
Takes values "CM", "LR" or "both" if only Concordant Mutations test, or only Likelihood Ratio test, or both should be performed. Default value is "both".
注意到价值观“CM”的“轻铁”或“两个”如果只谐和突变试验，或仅似然比检验，或者两者都应该被执行。默认值是“两者”。
Details
详情----------Details----------
Function tests clonality of LOH profiles of tumors from the same patient using two tests. Concordant Mutations test has number of markers with concordant LOH as its test statistic. Its theoretical reference distribution under independence is calculated assuming that the maternal and paternal alleles are equally likely to be lost and that the frequencies of LOH are about the same across different markers.
功能测试的克隆蕙型材使用两个测试从同一病人的肿瘤。一致突变试验作为检验统计量的一致蕙标记的数量。其理论参考分布在独立的计算假设，母亲和父亲的等位基因也同样可能会丢失，LOH的频率是在不同的标记相同。
Likelihood Ratio test uses pre-specified frequencies of LOH to compute Likelihood Ratio statistic. Its reference distrbution is obtained by simulating tumors with the given LOH probabilities, and probability of maternal/paternal mutation estimated from the data. If LOH frequencies are not specified then they are estimated from the data.
似然比检验使用蕙预先指定的频率来计算似然比统计。其参考平均每人所得分配是通过模拟与蕙概率肿瘤，并从数据估计的母亲/父亲的基因突变的概率。如果没有指定，那么LOH频率他们估计的数据。
值----------Value----------
The function returns a data frame where each row corresponds to the pair of samples that are compared. Columns are: Sample1 - name of sample 1; Sample2 - name of sample 2; a - number of markers with concordant LOH in both tumors (test statistic for Concordant Mutations test); e - number of markers with LOH in both tumors, concordant or discordant; f - number of markers with LOH in the first tumor and Normal in the 2nd tumor; g - number of markers with LOH in the second tumor and Normal in the first tumor; h - number of markers that are Normal in both tumors; Ntot - total number of informative markers for both tumors; CMpvalue - p-value for Concordant Mutations test; LRpvalue - p-value for Likelihood Ratio test.
该函数返回一个数据框，其中的每一行对应于对样品比较。栏目有：样品1 - 样品1名;的sample2 - 样品2名; - 标记数目一致的两个肿瘤蕙（为谐和突变试验测试统计）; E - 蕙两个肿瘤标志物，一致或不和谐的; F - 蕙在第一肿瘤标志物和第二肿瘤的正常; G - 蕙在第一个肿瘤，H在第二肿瘤和正常的标记 - 标记在两个肿瘤师范大学数数; ntot - 信息标记为肿瘤的总数; CMpvalue - 谐和突变试验的p值; LRpvalue - 似然比检验的p值。
参考文献----------References----------
举例----------Examples----------
set.seed(25)
LOHtable<-cbind(1:20,matrix(sample(c(0,1,2),20*20,replace=TRUE),20))
LOHclonality(LOHtable,rep(1:10,each=2),pfreq=NULL,noloh=0,loh1=1,loh2=2)
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 2012-2-25 15:11:06
