wilc.stat(siggenes)
wilc.stat()所属R语言包：siggenes
SAM Analysis Using Wilcoxon Rank Statistics
SAM的分析，利用秩统计
译者：生物统计家园网 机器人LoveR
描述----------Description----------
Generates the required statistics for a Significance Analysis of Microarrays analysis using standardized Wilcoxon rank statistics.
产生的微阵列分析的意义，使用标准化的秩统计分析所需的统计资料。
Should not be called directly, but via sam(..., method = wilc.stat).
不应该被称为直接，但通过SAM（...，方法= wilc.stat）。
用法----------Usage----------
wilc.stat(data, cl, gene.names = NULL, R.fold = 1, use.dm = FALSE,
R.unlog = TRUE, na.replace = TRUE, na.method = "mean",
approx50 = TRUE, ties.method=c("min","random","max"),
use.row = FALSE, rand = NA)
参数----------Arguments----------
参数：data
a matrix or a data frame. Each row of data must correspond to a variable (e.g., a gene), and each column to a sample (i.e.\ an observation).
矩阵或一个数据框。每行data必须符合变量（例如，一个基因），每个样品的列（即\观察）。
参数：cl
a numeric vector of length ncol(data) containing the class labels of the samples. In the two class paired case, cl can also be a matrix with ncol(data) rows and 2 columns. For details on how cl should be specified, see ?sam.
一个长度为数字向量ncol(data)样品含有类的标签。在这两个类的配对病例，cl也可以是一个ncol(data)行2列的矩阵。如何cl应指定的详细信息，请参阅?sam。
参数：gene.names
a character vector of length nrow(data) containing the names of the genes.
特征向量的长度nrow(data)包含的基因的名称。
参数：R.fold
a numeric value. If the fold change of a gene is smaller than or equal to R.fold, or larger than or equal to 1/R.fold,respectively, then this gene will be excluded from the SAM analysis. The expression score d of excluded genes is set to NA. By default, R.fold is set to 1 such that all genes are included in the SAM analysis. Setting R.fold to 0 or a negative value will avoid the computation of the fold change. The fold change is only computed in the two-class unpaired case.
一个数值。倍，如果一个基因的变化小于或等于R.fold或大于或等于1 / R.fold“，那么这种基因将被排除从SAM分析。排除基因的表达得分d设置为NA。默认情况下，R.fold设置为1，所有的基因都包括在SAM分析。设置R.fold0或负数，将避免倍计算。在两个阶级的未成的情况下，只计算倍。
参数：use.dm
if TRUE, the fold change is computed by 2 to the power of the difference between the mean log2 intensities of the two groups, i.e.\ 2 to the power of the numerator of the test statistic. If FALSE, the fold change is determined by computing 2 to the power of data (if R.unlog = TRUE) and then calculating the ratio of the mean intensity in the group coded by 1 to the mean intensity in the group coded by 0. The latter is the default, as this definition of the fold change is used in Tusher et al.\ (2001).
如果TRUE，2倍计算平均的log2强度两组之间的差异的力量，即\ 2检验统计量的分子的力量。如果FALSE如果data），然后计算的平均强度在1编码的组比例平均计算电源R.unlog = TRUE（2倍确定强度由0编码组。后者是默认的，这个定义的fold change在Tusher等使用。\（2001年）。
参数：R.unlog
if TRUE, the anti-log of data will be used in the computation of the fold change. Otherwise, data is used. This transformation should be done if data is log2-tranformed. (In a SAM analysis, it is highly recommended to use log2-transformed expression data.) Ignored if use.dm = TRUE.
如果TRUE，data反log将用于计算倍。否则，data使用。这种转变应做data如果是log2 tranformed的。 （在SAM分析，强烈建议使用log2转化表达数据。）如果use.dm = TRUE忽略。
参数：na.replace
if TRUE, missing values will be removed by the genewise/rowwise statistic specified by na.method. If a gene has less than 2 non-missing values, this gene will be excluded from further analysis. If na.replace = FALSE, all genes with one or more missing values will be excluded from further analysis. The expression score d of excluded genes is set to NA.
如果TRUE，遗漏值将被删除由na.method指定2-6。/ rowwise统计。如果一个基因具有非缺失值小于2，这种基因将被排除在进一步分析。如果na.replace = FALSE，缺少一个或多个值的基因将被排除进一步分析。排除基因的表达得分d设置为NA。
参数：na.method
a character string naming the statistic with which missing values will be replaced if na.replace=TRUE. Must be either "mean" (default) or median.
命名的统计与缺失值将被替换的字符串，如果na.replace=TRUE。必须要么"mean"（默认）或median。
参数：approx50
if TRUE, the null distribution will be approximated by the standard normal distribution. Otherwise, the exact null distribution is computed. This argument will automatically be set to FALSE if there are less than 50 samples in each of the groups.
如果TRUE，空分布将近似标准正态分布。否则，计算精确的空分布。此参数将被自动设置为FALSE如果有小于50，在各组样品。
参数：ties.method
either "min" (default), "random", or "max". If "random", the ranks of ties are randomly assigned. If "min" or "max", the ranks of ties are set to the minimum or maximum rank, respectively. For details, see the help of rank. If use.row = TRUE, ties.method = "max" will be used. For the handling of Zeros, see Details.
要么"min"（默认），"random"或"max"。如果"random"，被随机分配关系的行列。如果"min"或"max"，队伍的关系设置为最小或最大的排名分别。有关详情，请参阅帮助rank。如果use.row = TRUE，ties.method = "max"将被使用的。对于零点的处理，看到详细信息。
参数：use.row
if TRUE, rowWilcoxon is used to compute the Wilcoxon rank statistics.
如果TRUE，rowWilcoxon用来计算秩统计。
参数：rand
numeric value. If specified, i.e. not NA, the random number generator will be set into a reproducible state.
数值。如果指定，即不NA，随机数发生器将被设置成一个可重复的状态。
Details
详情----------Details----------
Standardized versions of the Wilcoxon rank statistics are computed. This means that W* = (W - mean(W)) / sd(W) is used as expression score d, where W is the usual Wilcoxon rank sum statistic or Wilcoxon signed rank statistic, respectively.
计算秩统计信息的标准化版本。这意味着，W* = (W - mean(W)) / sd(W)表达得分d，其中W是平时的秩的总和统计或Wilcoxon符号秩统计，分别。
In the computation of these statistics, the ranks of ties are by default set to the minimum rank. In the computation of the Wilcoxon signed rank statistic, zeros are randomly set either to a very small positive or negative value.
在这些统计数据的计算，队伍的关系是默认设置的最低排名。 Wilcoxon符号秩统计量的计算，零随机设置一个很小的正值或负值。
If there are less than 50 observations in each of the groups, the exact null distribution will be used. If there are more than 50 observations in at least one group, the null distribution will by default be approximated by the standard normal distribution. It is, however, still possible to compute the exact null distribution by setting approx50 to FALSE.
如果有小于50在各组的意见，确切的空分布将被使用。如果有超过50至少有一组的意见，空分布将默认情况下，可以通过标准正态分布近似。然而，它仍然有可能通过设置approx50FALSE的空分布的确切计算。
值----------Value----------
A list containing statistics required by sam.
列表包含sam需要的统计数据。
作者（S）----------Author(s)----------
Holger Schwender, <a href="mailto:holger.schw@gmx.de">holger.schw@gmx.de</a>
参考文献----------References----------
the Empirical Bayes and the Significance Analysis of Microarrays. Technical Report, SFB 475, University of Dortmund, Germany.
applied to the ionizing radiation response. PNAS, 98, 5116-5121.
参见----------See Also----------
SAM-class,sam, wilc.ebam
SAM-class，sam，wilc.ebam
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。
|
发表于 2012-2-26 14:16:20
