toptable(limma)
toptable()所属R语言包：limma
Table of Top Genes from Linear Model Fit
线性模型拟合热门的基因表
译者：生物统计家园网 机器人LoveR
描述----------Description----------
Extract a table of the top-ranked genes from a linear model fit.
从线性模型的拟合排名第一的基因提取表。
用法----------Usage----------
topTable(fit, coef=NULL, number=10, genelist=fit$genes, adjust.method="BH",
sort.by="B", resort.by=NULL, p.value=1, lfc=0, confint=FALSE)
toptable(fit, coef=1, number=10, genelist=NULL, A=NULL, eb=NULL, adjust.method="BH",
sort.by="B", resort.by=NULL, p.value=1, lfc=0, confint=FALSE, ...)
topTableF(fit, number=10, genelist=fit$genes, adjust.method="BH",
sort.by="F", p.value=1, lfc=0)
topTreat(fit, coef=1, number=10, genelist=fit$genes, adjust.method="BH",
sort.by="p", resort.by=NULL, p.value=1)
参数----------Arguments----------
参数：fit
list containing a linear model fit produced by lmFit, lm.series, gls.series or mrlm. For topTable, fit should be an object of class MArrayLM as produced by lmFit and eBayes.
列表中包含一个线性模型拟合lmFit，lm.series，gls.series或mrlm。 topTable，fit应该是一个类的对象MArrayLMlmFit和eBayes生产。
参数：coef
column number or column name specifying which coefficient or contrast of the linear model is of interest. For topTable, can also be a vector of column subscripts, in which case the gene ranking is by F-statistic for that set of contrasts.
列数或列名指定系数线性模型的对比是利益。为topTable，也可以是一个列标向量，在这种情况下，基因的排名是由F-统计，对比。
参数：number
maximum number of genes to list
列出的最大数量的基因
参数：genelist
data frame or character vector containing gene information. For topTable only, this defaults to fit$genes.
数据框或特征向量包含的基因信息。 topTable，默认fit$genes。
参数：A
matrix of A-values or vector of average A-values. For topTable only, this defaults to fit$Amean.
矩阵A值或平均A值向量。 topTable，默认fit$Amean。
参数：eb
output list from ebayes(fit). If NULL, this will be automatically generated.
输出列表从ebayes(fit)。如果NULL，这将自动生成。
参数：adjust.method
method used to adjust the p-values for multiple testing. Options, in increasing conservatism, include "none", "BH", "BY" and "holm". See p.adjust for the complete list of options. A NULL value will result in the default adjustment method, which is "BH".
方法采用P-值调整为多个测试。选项，在越来越保守，包括"none"，"BH"，"BY"和"holm"。看到p.adjust选项的完整列表。一个NULL值将导致在默认的调整方法，这是"BH"。
参数：sort.by
character string specifying statistic to rank genes by. Possibilities for topTable and toptable are "logFC", "AveExpr", "t", "P", "p", "B" or "none". "M" is allowed as a synonym for "logFC" for backward compatibility. Other permitted synonyms are "A" or "Amean" for "AveExpr", "T" for "t" and "p" for "P". Possibilities for topTableF are "F" or "none". Possibilities for topTreat are as for topTable minus "B".
字符串指定统计排名基因。可能性topTable和toptable是"logFC"，"AveExpr"，"t"，"P"，"p"，"B"或"none"。 "M"允许作为"logFC"向后兼容的代名词。其他允许的同义词是"A"或"Amean""AveExpr"，"T""t"和"p""P"。 topTableF可能性"F"或"none"。 topTreat可能性为topTable减"B"。
参数：resort.by
character string specifying statistic to sort the selected genes by in the output data.frame. Possibilities are the same as for sort.by.
字符串指定的统计，在输出数据框选定的基因排序。可能性是作为sort.by一样。
参数：p.value
cutoff value for adjusted p-values. Only genes with lower p-values are listed.
调整p值的临界值。只有较低的P-值的基因列出。
参数：lfc
minimum absolute log2-fold-change required. topTable and topTableF include only genes with (at least one) absolute log-fold-changes greater than lfc. topTreat does not remove genes but ranks genes by evidence that their log-fold-change exceeds lfc.
所需的最低绝对的log2倍变化。 topTable和topTableF包括唯一的基因（至少一个）绝对比lfclog倍的变化更大。 topTreat不删除证据，他们的log倍变化超过lfc基因，但队伍的基因。
参数：confint
logical, should 95% confidence intervals be output for logFC?
逻辑，应该95％置信区间为logFC输出？
参数：...
any other arguments are passed to ebayes if eb is NULL
任何其他参数传递给ebayes如果eb是NULL
Details
详情----------Details----------
toptable is an earlier interface and is retained only for backward compatibility.
toptable是一个较早的接口，只保留向后兼容性。
This function summarizes a linear model fit object produced by lmFit, lm.series, gls.series or mrlm by selecting the top-ranked genes for any given contrast. topTable and topTableF assume that the linear model fit has already been processed by eBayes. topTreat assumes that the fit has been processed by treat.
此功能，总结了线性模型的拟合对象产生lmFit，lm.series，gls.series或mrlm排名第一的基因，对于任何给定的对比选择。 topTable和topTableF假设线性模型的拟合已经eBayes处理。 topTreat假设的适当处理已经由treat。
The p-values for the coefficient/contrast of interest are adjusted for multiple testing by a call to p.adjust. The "BH" method, which controls the expected false discovery rate (FDR) below the specified value, is the default adjustment method because it is the most likely to be appropriate for microarray studies. Note that the adjusted p-values from this method are bounds on the FDR rather than p-values in the usual sense. Because they relate to FDRs rather than rejection probabilities, they are sometimes called q-values. See help("p.adjust") for more information.
p值利息系数/对比度调整调用p.adjust由多个测试。 "BH"方法，它控制了预期的错误发现率低于指定值（FDR）的，是默认的调整方法，因为它是最有可能适合于芯片研究。请注意，这种方法的调整，从p值是对FDR的边界，而不是通常意义上的P-值。因为它们涉及到FDRs而不是排斥反应的概率，他们有时也被称为Q值。看到help("p.adjust")更多信息。
Note, if there is no good evidence for differential expression in the experiment, that it is quite possible for all the adjusted p-values to be large, even for all of them to be equal to one. It is quite possible for all the adjusted p-values to be equal to one if the smallest p-value is no smaller than 1/ngenes where ngenes is the number of genes with non-missing p-values.
注意，如果没有很好的证据，实验中的表达差，这是很可能调整后的P-值要大，甚至他们都等于一体，。这是很可能所有调整后的P-值等于一个最小的p值小于1/ngenes其中ngenes是不可缺失的P-值的基因数量。
The sort.by argument specifies the criterion used to select the top genes. The choices are: "logFC" to sort by the (absolute) coefficient representing the log-fold-change; "A" to sort by average expression level (over all arrays) in descending order; "T" or "t" for absolute t-statistic; "P" or "p" for p-values; or "B" for the lods or B-statistic.
sort.by参数指定使用的标准，选择顶部的基因。的选择是："logFC"排序（绝对）代表log倍变化系数;"A"平均表达水平（以上所有阵列）按降序排序，“"T"或"t"绝对的t-统计; "P"或"p"p值;或"B"lods或B-统计。
Normally the genes appear in order of selection in the output table. If a different order is wanted, then the resort.by argument may be useful. For example, topTable(fit, sort.by="B", resort.by="logFC") selects the top genes according to log-odds of differential expression and then orders the selected genes by log-ratio in decreasing order. Or topTable(fit, sort.by="logFC", resort.by="logFC") would select the genes by absolute log-fold-change and then sort them from most positive to most negative.
正常基因出现在输出表中选择的顺序。如果想以不同的顺序，然后resort.by说法可能是有用的。例如，topTable(fit, sort.by="B", resort.by="logFC")选择顶部的基因根据登录的差异表达的可能性，然后订单数比依次选定的基因。或topTable(fit, sort.by="logFC", resort.by="logFC")会选择绝对log倍变化的基因，然后从最积极最负对其进行排序。
topTableF ranks genes on the basis of moderated F-statistics for one or more coefficients. If topTable is called with coef has length greater than 1, then the specified columns will be extracted from fit and topTableF called on the result. topTable with coef=NULL is the same as topTableF, unless the fitted model fit has only one column.
topTableF的行列基因上的一个或多个系数放缓F-统计的基础。如果topTable被称为“coef有长度大于1，则指定的列将fit和topTableF结果称为提取。 topTablecoef=NULL是一样的topTableF，除非拟合模型fit只有一列的。
Toptable output for all probes in original (unsorted) order can be obtained by topTable(fit,sort="none",n=Inf). However write.fit or write may be preferable if the intention is to write the results to a file. A related method is as.data.frame(fit) which coerces an MArrayLM object to a data.frame.
toptable输出为原始（未分类）中的所有探针可以得到topTable(fit,sort="none",n=Inf)。然而write.fit或write可能是可取的，如果意图是将结果写入一个文件。一个相关的方法是as.data.frame(fit)胁迫MArrayLM对象数据框。
By default number probes are listed. Alternatively, by specifying p.value and number=Inf, all genes with adjusted p-values below a specified value can be listed.
默认情况下，number探针。另外，通过指定p.value和number=Inf，调整p值低于指定值的所有基因，可以上市。
The argument lfc gives the ability to filter genes by log-fold change. This argument is not available for topTreat because treat already handles fold-change thresholding in a more sophisticated way.
参数lfc给人的能力来过滤log倍变化的基因。这种说法是不topTreat因为treat已经处理更复杂的方式倍数变化阈值。
值----------Value----------
Produces a dataframe with a row for the number top genes and the following columns:
产生了一排number顶级基因和后列dataframe：
参数：genelist
one or more columns of probe annotation, if genelist was included as input
被列入作为输入一个或多个列探针注释，如果genelist
参数：logFC
estimate of the log2-fold-change corresponding to the effect or contrast (for topTableF there may be several columns of log-fold-changes)
估计的log2倍的变化，相应的效果或对比（topTableFlog倍的变化有可能是几列）
参数：CI.025
left limit of confidence interval for logFC (if contint=TRUE)
左极限信心区间logFC（如果contint=TRUE）
参数：CI.975
right limit of confidence interval for logFC (if contint=TRUE)
右极限的信心区间logFC（如果contint=TRUE）
参数：AveExpr
average log2-expression for the probe over all arrays and channels, same as Amean in the MarrayLM object
平均的log2超过所有的阵列和渠道探针，AmeanMarrayLM对象相同的表达
参数：t
moderated t-statistic (omitted for topTableF)
t-统计放缓（省略topTableF）
参数：F
moderated F-statistic (omitted for topTable unless more than one coef is specified)
主持的F-统计（topTable除非指定了一个以上的系数是省略）
参数：P.Value
raw p-value
原料供磷值
参数：adj.P.Value
adjusted p-value or q-value
调整后的P-值或Q值
参数：B
log-odds that the gene is differentially expressed (omitted for topTreat)
log几率的基因差异表达（topTreat省略）
作者（S）----------Author(s)----------
Gordon Smyth
参见----------See Also----------
An overview of linear model and testing functions is given in 06.LinearModels. See also p.adjust in the stats package.
线性模型和测试功能概述给出在06.LinearModels。也看到p.adjuststats包。
举例----------Examples----------
# See lmFit examples[lmFit例子]
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 23:28:00
