globaltest(globaltest)
globaltest()所属R语言包：globaltest
Global Test (Deprecated)
全球测试（已过时）
译者：生物统计家园网 机器人LoveR
描述----------Description----------
In microarray data, tests a (list of) group(s) of genes for significant association with a given clinical variable.
在微阵列数据，测试（名单）一个给定的临床变量的显着关联的基因组（S组）。
用法----------Usage----------
levels, d, event = 1, adjust,
method = c("auto", "asymptotic", "permutations", "gamma"),
参数----------Arguments----------
参数：X
Either a matrix of gene expression data, where columns correspond to samples and rows to genes or a Bioconductor ExpressionSet. The data should be properly normalized beforehand (and log- or otherwise transformed), but missing values are allowed (coded as NA). Gene and sample names can be included as the row and column names of X.
无论是基因表达数据矩阵，列对应的基因或样本和行1的BioconductorExpressionSet。数据应正确归事前（log或以其他方式改变），但允许缺失值（NA编码）。基因和样本的名称，可以包含作为X行和列的名称。
参数：Y
A vector with the clinical outcome of interest, having one value for each sample. If X is an ExpressionSet it can also be the name of a covariate in the phenoData from the ExpressionSet, or a formula object using these names. If the clinical outcome is survival, Y should contain the survival times.
与临床疗效的利益的向量，有一个为每个采样值。如果X是ExpressionSet它也可以在的phenoData或ExpressionSet对象，使用这些名称formula从协的名称。如果临床结果是求生存，以Y应该包含的生存时间。
参数：genesets
Either a vector or a list of vectors. Indicates the group(s) of genes to be tested. Each vector in genesets can be given in three formats. Either it can be a vector with 1 (TRUE) or 0 (FALSE) for each gene in X, with 1 indicating that the gene belongs to the group. Or it can be a vector containing the column numbers (in X) of the genes belonging to the group. Or it can be a subset of the rownames or featureNames for X.
无论是向量或向量列表。表示要测试的基因组（S）。每个genesets向量可以在三种格式。或者它可以是一个向量1（TRUE）或0（FALSE）每个基因在X1表明该基因属于组。或者它可以是一个向量，属于基因组包含的列数（在X）。或者它可以是一个子集的rownames或featureNamesX。
参数：model
Globaltest will try to determine the correct model from the input of Y and d. To override the automatic choice, use model = "logistic" for a two-valued outcome Y, model = "linear" for a continuous outcome and model = "survival" for a survival outcome.
globaltest将尝试确定从Y和d输入正确的模型。要覆盖自动选择，使用model = "logistic"两个值的结果Y，model = "linear"连续结果和model = "survival"生存结果。
参数：levels
If Y is a factor (or a category in the PhenoData slot of X) and contains more than 2 levels: levels is a vector of levels of Y to test. If levels is length 2: test these 2 groups against each other. If levels is length 1: test that level against the others.
如果Y是一个因素（或一类的XPhenoData插槽），并包含超过2级：levels是Y测试水平的向量。 levels如果是长度为2：测试这2组互相。如果水平是长度为1：测试，对别人的水平。
参数：d
A vector or the name of a covariate in the phenoData from the ExpressionSet X, to indicate which samples experienced an event. Providing a value for d automatically sets model = "survival"
向量或协变量的名称phenoData的ExpressionSetX，表明样品经历的事件。提供一个值d自动设置model = "survival"
参数：event
The value or values of d that indicates that there was an event.
值或d，值表明，有一个事件。
参数：adjust
Confounders or risk factors for which the test must be adjusted. Must be either a data frame or (if X is an ExpressionSet) the names of covariates in the phenoData from X or a formula object using these names. Default: no adjustment.
测试必须调整混杂因素或危险因素。必须有一个数据框或（如果X是ExpressionSet）的名称中的phenoData协变量X或formula对象使用这些名称。默认是：不作调整。
参数：method
The method for calculation the p-value. Use method = "asymptotic" for the full asymptotic distribution of the test statistic; method = "gamma" for the gamma (= scaled chi-squared) approximation to that distribution and method = "permutations" for a permutation p-value. The default: method = "auto" chooses the permutations method if the number of possible permutations does not exceed 10,000 and the asymptotic otherwise. Note that method = "gamma" was the default option prior to version 4.0.0.
计算p值的方法。使用method = "asymptotic"完整的检验统计量的渐近分布; method = "gamma"，分布和伽玛（=缩放卡方）逼近method = "permutations"置换p值。默认的：method = "auto"选择的排列方法，如果可能的排列数量不超过10,000元及渐近，否则的。请注意，method = "gamma"版本4.0.0之前是默认选项。
参数：nperm
A number of permutations. This gives the (maximum) number of permutations to be used if method = "permutations" or method = "auto".
一些排列。这使得要使用的排列（最大）数目，如果method = "permutations"或method = "auto"。
参数：scaleX
If true, rescales the expression matrix to get pleasant value for all test statistics. The expression matrix X is multiplied by a constant in such a way that the expected value EQ of the test statistic for the global test becomes exactly 10. This rescaling has no effect on the p-values.
如果属实，重新调整表达矩阵所有测试统计中得到愉快的价值。表达矩阵X乘以常数在这样一种方式，全球测试情商的检验统计量的期望值变得整整10。这个缩放功能有没有p值的影响。
参数：accuracy
Numerical tuning parameter useable only with the asymptotic method and a non-survival response. Determines how much small eigenvalues of the R matrix are smoothed away to increase computation speed. Choose smaller values for quicker computations but conservative p-values; choose larger values for slower calculations but more accuracy.
只用渐近方法和非生存的响应可用的数值调整参数。确定R矩阵小特征值多少进行平滑处理，提高运算速度。选择更快的计算，但保守的p值较小的值，计算速度较慢，但更准确选择较大的值。
参数：...
Captures deprecated input for compatibility with older versions of globaltest. </table>
捕获废弃输入与旧版本globaltest的兼容性。 </ TABLE>
Details
详情----------Details----------
The Global Test tests whether a group of genes (of any size from one single gene to all genes on the array) is significantly associated with a clinical variable. The group could be for example a known pathway, an area on the genome or the set of all genes. The test investigates whether samples with similar clinical outcomes tend to have similar gene expression patterns. For a significant result it is not necessary that the genes in the group have similar expression patterns, only that many of them are correlated with the outcome.
全球测试测试是否显着的临床变量相关的基因组（任何从一个单一的基因阵列上的所有基因的大小）。组，例如可能是一个已知的途径，对基因组的所有基因组领域。测试调查样本是否具有相似的临床结果往往有相似的基因表达模式。一个显着的结果是没有必要的，该组中的基因有类似的表达方式，只是他们中的许多相关的结果。
值----------Value----------
The function returns an object of class
该函数返回一个类的对象
注意----------Note----------
globaltest has been deprecated. Please use gt instead.
globaltest已被弃用。请使用gt代替。
The options globaltest options sampling and permutation have been replaced by separate functions from version 3.0. See
从3.0版本的独立的功能已被替换的选项globaltest选项采样和置换。见
作者（S）----------Author(s)----------
Jelle Goeman: <a href="mailto:j.j.goeman@lumc.nl">j.j.goeman@lumc.nl</a>; Jan Oosting
参考文献----------References----------
参见----------See Also----------
Many more examples in the vignette! geneplot, sampleplot, sampling, gt.multtest, permutations,
更多的例子中的小插曲！ geneplot，sampleplot，sampling，gt.multtest，permutations
举例----------Examples----------
# Breast cancer data (ExpressionSet) from the Netherlands Cancer[从荷兰癌症乳腺癌数据（ExpressionSet）]
# Institute with annotation:[研究所与注释：]
data(vandeVijver)
data(annotation.vandeVijver)
# Many possible calls. See the vignette for more examples and explanation.[许多可能的调用。看到更多的例子和解释的小插曲。]
globaltest(vandeVijver, "StGallen")
globaltest(vandeVijver, "StGallen", annotation.vandeVijver)
globaltest(vandeVijver, "Surv(TIMEsurvival, EVENTdeath)", annotation.vandeVijver)
globaltest(vandeVijver, StGallen ~ Posnodes + StGallen, annotation.vandeVijver)
globaltest(vandeVijver, "StGallen", method = "p")
# Store the test result[存储测试结果]
# See help(gt.result) for more options[请参阅帮助更多的选择（gt.result）]
gt <- globaltest(vandeVijver, "StGallen", annotation.vandeVijver)
gt[1:2]
sort(gt)
p.value(gt)
# Also with simple vector/matrix input[还具有简单的向量/矩阵输入]
X <- matrix(rnorm(3000), 100, 30) # random expression data[随机表达数据]
Y <- 1:30 # a response variable[响应变量]
pathway <- 1:40 # a pathway[一个途径]
globaltest(X, Y)
globaltest(X, Y, pathway)
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 20:43:03
