summarize.clones(aCGH)
summarize.clones()所属R语言包：aCGH
Extracting summary information for all clones
所有克隆提取摘要信息
译者：生物统计家园网 机器人LoveR
描述----------Description----------
summarize.clones function is the text equivalent of plotFreqStat function - it summarizes the frequencies of changes for each clone accross tumors and when available assigns statistics. The resulting table can be easily exported.
summarize.clones功能plotFreqStat函数的文本等效项 - 它总结每个的克隆accross肿瘤的变化频率和时，可转让的统计数字。结果表可以很容易地导出。
用法----------Usage----------
summarize.clones(aCGH.obj, resT = NULL, pheno = rep(1, ncol(aCGH.obj)), rsp.uniq = unique(pheno), thres = 0.25, factor = 2.5, all = length(rsp.uniq) == 1 && is.null(resT), titles = if (all) "all" else rsp.uniq)
参数----------Arguments----------
参数：aCGH.obj
aCGH.obj object here
aCGH.obj反对在这里
参数：resT
Data frame having the same structure as the result of applying mt.maxT or mt.minP functions from Bioconductor's multtest package for multiple testing. The result is a data frame including the following 4 components: 'index', 'teststat', 'rawp' and 'adjp'.Default is the unique levels of the phenotype. Not used when all is TRUE.
数据框申请mt.maxT或mt.minPBioconductor的multtest多个测试包功能的结果具有相同的结构。结果是一个数据框包括以下4部分组成：“索引”，“teststat，rawp”和“adjp”默认的表型是独特的水平。不使用时all为TRUE。
参数：pheno
phenotype to compare
表型比较
参数：rsp.uniq
rsp.uniq specified the codes for the groups of interest. Default is the unique levels of the phenotype. Not used when all is TRUE.
rsp.uniq指定为利益团体的代码。默认是独特的表型水平。不使用时all为TRUE。
参数：thres
thres is either a vector providing unique threshold for each sample or a vector of the same length as number of samples (columns in data) providing sample-specific threshold. If aCGH.obj has non-null sd.samples, then threshold is automatically replaced by tumor-specific sd multiplied by factor. Clone is considered to be gained if it is above the threshold and lost if it below negative threshold. Defaults to 0.25
thres要么是矢量提供独特的阈值，每个样品或提供样品特定的阈值样本数（data列）相同长度的向量。 aCGH.obj如果有非空sd.samplesfactor，然后阈值自动替换肿瘤特异性SD乘以。克隆被认为是上涨，如果它上面的阈值和丢失，如果它的阈值低于负。默认为0.25
参数：factor
factor specifies the number by which experimental variability should be multiples. used only when tumor specific variability in aCGH.obj is not NULL. Defaults to 2.5
factor指定的实验变异应该是倍数。仅用于肿瘤aCGH.obj特定变异时是不是NULL。默认2.5
参数：all
all specifies whether samples should be analyzed by subgroups (TRUE) or together (FALSE)
all指定样品是否应进行分组（真）或（假）
参数：titles
titles names of the groups to be used. Default is the unique levels of the pheno.
titles要使用的组的名称。默认是pheno独特的水平。
值----------Value----------
Returns matrix containg the following information for each clones: annotation (same as in clones.info), number and proportion of samples where clone is present,gained and lost; and the same in each group if more than one group. Additionally, if significance comparison has been done, value of the statistic, unadjusted p-value and adjusted p-values are included for each clone.
返回矩阵containg每个克隆的以下信息：注释（一样在clones.info），数量和比例克隆是目前的样品，获得和丢失;在各组相同，如果超过一组。此外，如果已经做了比较意义，统计值，p值未调整和调整后的P-值包括为每个克隆。
作者（S）----------Author(s)----------
Jane Fridlyand
参见----------See Also----------
plotFreqStat, aCGH
plotFreqStat，aCGH
举例----------Examples----------
data(colorectal)
summarize.clones(colorectal)
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 11:01:21
