copa(copa)
copa()所属R语言包：copa
Calculate COPA Scores from a Set of Microarrays
COPA的成绩计算由一组微阵列
译者：生物统计家园网 机器人LoveR
描述----------Description----------
This function calculates COPA scores from a set of microarrays. Input can be an ExpressionSet, or a matrix or data.frame.
此函数计算COPA的成绩，从一个芯片集。输入可以是ExpressionSet，或矩阵或data.frame。
用法----------Usage----------
copa(object, cl, cutoff = 5, max.overlap = 0, norm.count = 0, pct = 0.95)
参数----------Arguments----------
参数：object
An ExpressionSet, or a matrix or data.frame.
ExpressionSet，或矩阵或data.frame。
参数：cl
A vector of classlabels indicating sample status (normal = 1, tumor = 2).
classlabels的指示样品状态（正常= 1，肿瘤= 2）的向量。
参数：cutoff
The cutoff to determine 'outlier' status. See details for more information.
截止到确定“离群”的状态。详情请参阅更多信息。
参数：max.overlap
The maximum number of samples that can be considered 'outliers' when comparing two genes. The default is 0, indicating that there can be no overlap. See details for more information.
可以被认为是“离群值”时，比较两种基因样本的最大数量。默认为0，表明不可能有重叠。详情请参阅更多信息。
参数：norm.count
The number of normal samples that can be considered 'outliers'. The default is 0, meaning that no normals may be outliers.
正常，可以认为是“离群”的样品数。默认为0，也就是说，没有法线可能离群。
参数：pct
The percentile to use for pre-filtering the data. A preliminary step is to compute the number of outlier samples for each gene. All genes with a number of outlier samples less than the (default 95th) percentile will be removed from further consideration.
百分用于预过滤数据。一个初步的一步是计算每个基因离群样本数量。将删除所有基因的离群样本数量小于（默认95）百分进一步审议。
Details
详情----------Details----------
Cancer Outlier Profile Analysis is a method that is intended to find pairs of genes that may be involved in recurrent gene fusion with a third (unknown) gene. The underlying idea here is that in certain cancers it may be common for the promoter region of one gene to become fused to certain oncogenes. For instance, Tomlins et. al. showed that the promoter region of TMPRSS2 fused to either ERG or ETV1 in the majority of prostate cancer tumors tested.
癌症离群资料分析是一种方法，目的是要找到第三（未知）基因可能参与经常性的基因融合基因对。这里的基本思想是，在某些癌症，它可能会成为某些癌基因融合到一个基因的启动子区域的共同。例如，Tomlins等。等。 TMPRSS2子区域融合在大多数前列腺癌肿瘤ERG或者ETV1测试表明。
Since this fusion should only happen with one oncogene in a given sample, we look for pairs of genes where some samples have much higher expression values, but the samples for gene 'A' are mutually exclusive from the samples for gene 'B'.
由于这种融合应该只有一个基因发生在一个给定的样本，我们期待对其中部分样品有更高的表达值的基因，但基因样本“A”基因“B”样本相互排斥。
The cutoff argument for this function is used to determine how high the centered and scaled expression value has to be in order to be considered an outlier. The max.overlap argument allows one to relax the requirement of mutual exclusivity, although in practice this is probably not advisable.
此函数的截止参数是用来确定中心和规模化的表达价值有多高，是为了被视为离群值。 max.overlap参数允许一个放松的相互排斥的要求，但在实践中，这可能是不可取的。
Note that this function computes all row-wise comparisons, which gets very large very quickly. The function will throw a warning for any data set containing > 1000 rows and query the user to see if he/she really wants to proceed. The number of genes to be considered can be adjusted by increasing/decreasing the 'pct' argument.
请注意，此函数计算所有行比较明智的，变得非常大，非常快。该函数将抛出的任何数据集，其中包含1000行的警告和查询，用户可以看到如果他/她真的想继续。要考虑的基因数目可以调整增加/减少％的说法。
值----------Value----------
参数：ord.prs
A matrix with two columns containing the ordered row numbers from the original matrix of gene expression values.
一个有两个有序的行数从原来的基因表达值矩阵列的矩阵。
参数：pr.sums
A numeric vector with the number of mutually exclusive outliers for each gene pair. This is the criterion for ranking the gene pairs; the assumption being that a pair of genes with more mutually exclusive outliers will be more interesting than a pair with relatively fewer outliers.
与每个基因对相互排斥的离群数的数字向量。这是居基因对标准的假设是，一双以上相互排斥的离群点的基因会更有趣的比对相对较少的离群。
参数：mat
A matrix containing the filtered gene expression values.
A矩阵包含筛选基因的表达值。
参数：cl
The classlabel vector passed to copa
classlabel向量的传递copa的
参数：cutoff
The cutoff used
使用截止
参数：max.overlap
The value of max.overlap used
的使用max.overlap的价值
参数：norm.count
The value of norm.count used
价值norm.count
参数：pct
The percentile used in the pre-filtering step
预过滤步骤中使用的百分
作者（S）----------Author(s)----------
James W. MacDonald
参考文献----------References----------
factor genes in prostate cancer. Science. 2005 Oct 28;310(5748):644-8.
举例----------Examples----------
library(Biobase)
data(sample.ExpressionSet)
cl <- abs(3 - as.numeric(pData(sample.ExpressionSet)[,2]))
tmp <- copa(sample.ExpressionSet, cl)
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 15:48:33
