comp.stat(DEDS)
comp.stat()所属R语言包：DEDS
Computing Test Statistics for Differential Expression
计算测试统计差异表达
译者：生物统计家园网 机器人LoveR
描述----------Description----------
This function computes test statistics, e.g., t-statistics, F-statistics, SAM, fold changes, moderated t or F statistics, B statistics, for each row of a microarray data matrix.
此函数计算检验统计量，例如，t-统计量，F-统计，SAM的，褶皱的变化，缓和T或F统计，乙统计，微阵列数据矩阵的每一行。
用法----------Usage----------
comp.stat(X, L, test = c("t", "fc", "sam", "f", "modt", "modf", "B"), extra = NULL)
参数----------Arguments----------
参数：X
A matrix, with m rows corresponding to variables (hypotheses) and n columns to observations. In the case of gene expression data, rows correspond to genes and columns to mRNA samples. The data can be read using read.table.
一个矩阵，用m行相应的变量（假设）和n列观察。在基因表达数据的情况下，行对应mRNA样品的基因和列。可以读取数据，使用read.table。
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：test
A character string specifying the statistic to be used to test the null hypothesis of no association between the variables and the class labels.<br> <table summary="Rd table"> <tr> <td align="left"> test="t": </td><td align="left"> t-statistics; </td> </tr> <tr> <td align="left"> test="f": </td><td align="left"> F-statistics;</td> </tr> <tr> <td align="left"> test="fc":</td><td align="left"> fold changes;</td> </tr> <tr> <td align="left"> test="sam": </td><td align="left"> SAM-statistics; </td> </tr> <tr> <td align="left"> test="modt": </td><td align="left"> moderated t-statistics;</td> </tr> <tr> <td align="left"> test="modf": </td><td align="left"> moderated F-statistics; </td> </tr> <tr> <td align="left"> test="B": </td><td align="left"> B-statistics.</td> </tr> </table>
一个字符串指定的统计，被用来测试空假设之间没有关联的变量和类的标签。参考<table summary="Rd table"> <TR> <TD ALIGN="LEFT">test="t"：</ TD> <td ALIGN="LEFT"> t-统计量; </ TD> </ TR> <TR> <td ALIGN="LEFT">test="f"：</ TD> < TD对齐=“左”的F-统计; </ TD> </ TR> <TR> <TD ALIGN="LEFT">test="fc"：</ TD> <td ALIGN="LEFT">倍的变化</ TD> </ TR> <TR> <TD ALIGN="LEFT"> test="sam"：</ TD> <td ALIGN="LEFT"> SAM统计; </ TD> </ TR> <TR> <TD ALIGN="LEFT">test="modt"：</ TD> <TD ALIGN="LEFT">主持t-统计量; </ TD> </ TR> <TR> <TD对齐=“离开“>test="modf"：</ TD> <td ALIGN="LEFT">放缓F-统计; </ TD> </ TR> <TR> <td ALIGN="LEFT">test="B" ：</ TD> <TD ALIGN="LEFT">的B-统计</ TD> </ TR> </ TABLE>
参数：extra
Extra parameter needed for the test specified; see deds.genExtra.
需要额外的参数指定的测试;看到deds.genExtra。
Details
详情----------Details----------
The function comp.stat interfaces to a C function and computes various statistics for differential expression in the C environment and therefore faster than functions in R. However, functions in R that are implemented in the DEDS packages may have more flexibility in terms of specifications of arguments. Below is a table the details comp.stat and its equivalent R functions in the DEDS package. Note that all the R functions listed in the 2nd column of the table below return a function with bindings for a series of arguments which accept the microarray data matrix as its single argument and compute accordingly statistics. <br>
函数comp.stat一个C函数的接口，并计算在C环境下的差异表达，因此比在R的功能，但速度更快的各种统计数据，研发实现的功能是在DEDS的包可能在以下方面有更多的灵活性规格参数。下面是一个表的细节comp.stat及其在DEDS的包相当于R函数。请注意，下面的R表的第二列中列出的所有功能，返回绑定一个函数接受单个参数的微阵列数据矩阵的一系列参数，并计算相应的统计。参考
值----------Value----------
A vector of test statistics for each row of the matrix.
矩阵的每一行的统计测试向量。
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----------
data. Statistica Sinica 12, 31-46.
assessing differential expression in microarray experiments. http://www.statsci.org/smyth/pubs/ebayes.pdf
参见----------See Also----------
deds.genExtra, for B statistics: lm.series and ebayes
deds.genExtra，乙统计：lm.series和ebayes
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
# t statistics[t统计]
tstat <- comp.stat(X, L, test="t")
# SAM, fudge factor set as the median of pooled genewise standard deviations[SAM，捏造因素集，中位数汇集了2-6。标准偏差]
samstat <- comp.stat(X, L, test="sam")
# SAM, fudge factor set as the 90% of pooled genewise standard deviations[SAM，捏造为90％，汇集了2-6。标准偏差的因素集]
samstat <- comp.stat(X, L, test="sam", extra=c(0.9))
# moderated t[主持ţ]
modtstat <- comp.stat(X, L, test="modt")
# B, proportion of differentially expressed genes is set at default, 1%[，差异表达基因的比例设置在默认情况下，1％]
Bstat <- comp.stat(X, L, test="B")
# B, proportion of differentially expressed genes is set at 10%[，差异表达基因的比例定为10％]
Bstat <- comp.stat(X, L, test="B", extra=c(0.1))
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注：
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发表于 2012-2-25 16:21:59
