comp.SAM(DEDS)
comp.SAM()所属R语言包：DEDS
Computing SAM Statistics for Differential Expression
计算的SAM统计差异表达
译者：生物统计家园网 机器人LoveR
描述----------Description----------
comp.SAM returns a function of one argument. This function has a environment with bindings for a series of arguments (see below). It accepts a microarray data matrix as its single argument, when evaluated, computes SAM statistics for each row of the matrix.
comp.SAM返回一个参数的函数。此功能有一系列的参数（见下文）绑定的环境。它接受一个芯片作为其单个参数，计算时，计算矩阵的每一行的SAM统计数据矩阵。
用法----------Usage----------
comp.SAM(L = NULL, prob = 0.5, B = 200, stat.only = TRUE, verbose = FALSE,
deltas, s.step=0.01, alpha.step=0.01, plot.it=FALSE)
参数----------Arguments----------
参数：L
A vector of integers corresponding to observation (column) class labels. For k classes, the labels must be integers between 0 and k-1.
观察（列）类的标签对应的整数向量。对于k类，标签必须是0k-1之间的整数。
参数：prob
A numeric variable used to set the fudge factor s_0 in terms of the percentile of the standard deviations of the genes. If set as NULL, s_0 is calculated using the algorithm by Tusher et al. (see reference).
一个数字变量，用于设置蒙混因素s_0基因的百分标准偏差。如果设置为NULL，s_0计算由Tusher等的使用的算法。 （见参考文献）。
参数：B
The number of permutations. For a complete enumeration, B should be 0 (zero) or any number not less than the total number of permutations.
排列数。对于一个完整的枚举，B应该是0（零）或任何数量不超过总数的排列。
参数：stat.only
A logical variable, if TRUE, only statistics are calculated and returned; if FALSE, false discovery rates (FDRs) for a set of delta(deltas) are calculated and returned.
一个逻辑变量，如果TRUE，只统计计算并返回;如果FALSE，虚假的发现率为delta（deltas）计算集（FDRs）和返回。
参数：verbose
A logical variable, if TRUE, informative messages are printed during the computation process.
一个逻辑变量，如果TRUE，提示信息会在计算过程中打印。
参数：deltas
A vector of values for the threshold delta; see Tusher et al.
阈值向量delta; Tusher等。
参数：s.step
A numeric variable specifying the size of the moving window across the gene-wise standard deviations for the selection of the fudge factor s_0.
一个数字变量指定的整个基因明智的选择蒙混因素s_0的标准偏差的移动窗口的大小。
参数：alpha.step
A numeric variable specifying the increment of a percentile sequence between 0 and 1, from which the fudge factor will be chosen to minimize the coefficient of variation of statistics.
一个数字变量指定一个介于0和1，蒙混因素，以最大限度地减少统计数据的变异系数将选择的百分序列的增量。
参数：plot.it
A logical variable, if TRUE, a plot between the coefficient of variation and the percentile sequence will be made.
逻辑变量TRUE，如果，图之间的变异系数和百分序列进行。
Details
详情----------Details----------
The function returned by comp.SAM calculates SAM statistics for each row of the microarray data matrix, with bindings for L, prob, B, stat.only, verbose, deltas, s.step, alpha.step and plot.it. If quantile=NULL, the fudge factor s_0 is calculated as the percentile of the gene-wise standard deviations that minimizes the coefficient of variation of the statistics; otherwise s_0 is set as the specified percentile of standard deviations. If stat.only=T, only SAM statistics are returned; otherwise, permutation will be carried out to calculate the FDRs for a set of deltas specified and a FDR table will be returned in addition to the SAM statistics.
comp.SAM返回函数计算的微阵列数据矩阵的每一行SAM统计，绑定L，prob，B，stat.only，verbose，deltas，s.step，alpha.step和plot.it。如果quantile=NULL，蒙混因素s_0是明智的基因，最大限度地减少变异系数的统计标准偏差百分计算，否则s_0设置为指定的百分标准偏差。否则，如果stat.only=T，只有SAM统计数字返回;置换将开展为一组来计算的FDRsdeltas指定1的FDR表将SAM的统计，除了返回。
值----------Value----------
SAM returns a function (F) with bindings for a series of arguments. When stat.only=T, the function F when evaluated returns a numeric vector of SAM statistics; When stat.only=F, the function F when evaluated returns a list of the following components:
SAM返回一个（F）与一系列参数绑定的功能。当stat.only=T计算时，函数F返回一个SAM的统计的数字向量;当stat.only=F，计算时函数F返回了以下组件的列表：
参数：geneOrder
Order of genes in terms of differential expression;
为了在差异表达的基因;
参数：sam
Sorted SAM statistics;
排序SAM的统计数据;
参数：fdr.table
A matrix with columns: delta, no.significance, no.positive, no.negatvie, FDR(50%), FDR(90%).
Delta，no.significance，no.positive，no.negatvie，FDR（50％），FDR（90％）：一列的矩阵。
作者（S）----------Author(s)----------
Yuanyuan Xiao, <a href="mailto:yxiao@itsa.ucsf.edu">yxiao@itsa.ucsf.edu</a>, <br>
Jean Yee Hwa Yang, <a href="mailto:jean@biostat.ucsf.edu">jean@biostat.ucsf.edu</a>.
参考文献----------References----------
applied to the ionizing radiation response, PNAS, 98, 5116-5121.
参见----------See Also----------
comp.t
comp.t
举例----------Examples----------
X <- matrix(rnorm(1000,0,0.5), nc=10)
L <- rep(0:1,c(5,5))
# genes 1-10 are differentially expressed[差异表达基因的1-10]
X[1:10,6:10]<-X[1:10,6:10]+1
# two sample test, statistics only[只有两个样本测试，统计]
sam.fun <- comp.SAM(L)
sam.X <- sam.fun(X)
# two sample test, FDR[两个样本测试，FDR]
sam.fun <- comp.SAM(L, stat.only=FALSE, delta=c(0.1, 0.2, 0.5))
sam.X <- sam.fun(X)
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。
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发表于 2012-2-25 16:21:52
