d.stat(siggenes)
d.stat()所属R语言包：siggenes
SAM Analysis Using a Modified t-statistic
SAM的分析改进的t-统计
译者：生物统计家园网 机器人LoveR
描述----------Description----------
Computes the required statistics for a Significance Analysis of Microarrays (SAM) using either a (modified) t- or F-statistic.
计算的意义分析的微阵列（SAM）的使用（修改）T-或F-统计所需的统计资料。
Should not be called directly, but via the function sam.
不应该被称为直接，但通过功能SAM。
用法----------Usage----------
d.stat(data, cl, var.equal = FALSE, B = 100, med = FALSE, s0 = NA,
s.alpha = seq(0, 1, 0.05), include.zero = TRUE, n.subset = 10,
mat.samp = NULL, B.more = 0.1, B.max = 30000, gene.names = NULL,
R.fold = 1, use.dm = TRUE, R.unlog = TRUE, na.replace = TRUE,
na.method = "mean", rand = NA)
参数----------Arguments----------
参数：data
a matrix, data frame or ExpressionSet object. Each row of data (or exprs(data), respectively) must correspond to a variable (e.g., a gene), and each column to a sample (i.e.\ an observation).
一个矩阵，数据框或ExpressionSet对象。 data（或exprs(data)，分别）的每一行必须对应一个变量（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. If data is an ExpressionSet object, cl can also be a character string. 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。 data如果是ExpressionSet对象，cl也可以是一个字符串。如何cl应指定的详细信息，请参阅?sam。
参数：var.equal
if FALSE (default), Welch's t-statistic will be computed. If TRUE, the pooled variance will be used in the computation of the t-statistic.
如果FALSE（默认），韦尔奇的t-统计量的计算。如果TRUE，将用于合并方差t-统计量的计算。
参数：B
numeric value indicating how many permutations should be used in the estimation of the null distribution.
数值，指示应在空分布的估计使用多少排列。
参数：med
if FALSE (default), the mean number of falsely called genes will be computed. Otherwise, the median number is calculated.
如果FALSE（默认），讹称为基因的平均数量来计算。否则，中位数的计算方法。
参数：s0
a numeric value specifying the fudge factor. If NA (default), s0 will be computed automatically.
一个数值指定蒙混因素。如果NA（默认），s0将自动计算。
参数：s.alpha
a numeric vector or value specifying the quantiles of the standard deviations of the genes used in the computation of s0. If s.alpha is a vector, the fudge factor is computed as proposed by Tusher et al. (2001). Otherwise, the quantile of the standard deviations specified by s.alpha is used as fudge factor.
一个数字的向量或值指定的位数的基因在用于s0计算的标准偏差。如果s.alpha是一个向量，软糖因素计算由Tusher等建议。 （2001年）。否则，位数由s.alpha指定的标准偏差用作蒙混因素。
参数：include.zero
if TRUE, s0 = 0 will also be a possible choice for the fudge factor. Hence, the usual t-statistic or F statistic, respectively, can also be a possible choice for the expression score d. If FALSE, s0=0 will not be a possible choice for the fudge factor. The latter follows Tusher et al. (2001) definition of the fudge factor in which only strictly positive values are considered.
如果TRUE，s0= 0蒙混因素也将是一个可能的选择。因此，通常的t-统计或F统计量，分别为，也可以是表达得分d可能的选择。如果FALSE，s0=0不会蒙混因素是可能的选择。后者如下Tusher等。 （2001）的定义，只有严格正面的价值观被认为是在蒙混因素。
参数：n.subset
a numeric value indicating how many permutations are considered simultaneously when computing the p-value and the number of falsely called genes. If med = TRUE, n.subset will be set to 1.
一个数值，表示多少排列计算p值和虚假称为基因数目时，同时考虑。如果med = TRUE，n.subset将设置为1。
参数：mat.samp
a matrix having ncol(data) columns except for the two class paired case in which mat.samp has ncol(data)/2 columns. Each row specifies one permutation of the group labels used in the computation of the expected expression scores d.bar. If not specified (mat.samp=NULL), a matrix having B rows and ncol(data) is generated automatically and used in the computation of d.bar. In the two class unpaired case and the multiclass case, each row of mat.samp must contain the same group labels as cl. In the one class and the two class paired case, each row must contain -1's and 1's. In the one class case, the expression values are multiplied by these -1's and 1's. In the two class paired case, each column corresponds to one observation pair whose difference is multiplied by either -1 or 1. For more details and examples, see the manual of siggenes.
矩阵ncol(data)列，除了配对的两个类情况中，mat.sampncol(data)/ 2列。每一行指定一个用于计算预期表达分数d.bar组标签的排列。如果没有指定（mat.samp=NULL），矩阵B行ncol(data)是自动生成的，用于计算在d.bar。在两个类未成的情况下，多类情况，每行mat.sampcl必须包含同一组标签。在一类和两个类的配对病例，每行必须包含-1和1的。在一类的情况下，表达式的值乘以这些1和1。在这两个类配对的情况下，每一列对应一个观察对，其差额乘以-1或1。对于更多的细节和例子，看到手册siggenes。
参数：B.more
a numeric value. If the number of all possible permutations is smaller than or equal to (1+B.more)*B, full permutation will be done. Otherwise, B permutations are used. This avoids that B permutations will be used – and not all permutations – if the number of all possible permutations is just a little larger than B.
一个数值。如果所有可能的排列数小于或等于（1 +B.more）*B，全置换将完成。否则，使用B排列。这就避免了B排列将使用 - 而不是所有的排列组合 - 如果所有可能的排列数量只是一个小比B。
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：B.max
a numeric value. If the number of all possible permutations is smaller than or equal to B.max, B randomly selected permutations will be used in the computation of the null distribution. Otherwise, B random draws of the group labels are used. In the latter way of permuting it is possible that some of the permutations are used more than once.
一个数值。如果所有可能的排列数小于或等于B.max的，B随机选择的排列将在空分布的计算。否则，B随机组标签提请使用。在后者置换的方式，它是可能的排列有些使用一次以上。
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 cases.
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。只计算未成情况下，在两个阶级的fold change。
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 definition of the fold change 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。后者是在用于Tusher等倍的定义。\（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 when 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。这个转变应该做，当datalog2-tranformed的（在SAM分析，它是高度推荐使用的log2转化的基因表达数据）。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：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。
值----------Value----------
An object of class SAM.
类SAM的对象。
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, z.ebam
SAM-class，sam，z.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。
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发表于 2012-2-26 14:11:07
