barplotSignatures(phenoTest)
barplotSignatures()所属R语言包：phenoTest
Summary plots for gene signature vs phenotype association
基因签名与表型协会的概要图
译者：生物统计家园网 机器人LoveR
描述----------Description----------
Summarizes the univariate relationships between genes in one or more signatures and several phenotype variables, as summarized in epheno objects (which can be created with the ExpressionPhenoTest function).
总结基因之间的关系，在一个或多个签名和几个表型变量的单变量epheno（ExpressionPhenoTest函数可以创建对象）总结。
By default barplotSignifSignatures performs a binomial test (binom.test from package stats) for each signature to see if the number of up up regulated and down regulated genes is different enough to be statistically different. When a reference gene set is provided we test if the proportions of up and down regulated genes of each gene set is different from the proportions in the reference gene set. This has been done with a chi-square test. When a reference gene set is provided and parameter testUpDown is TRUE (by default its FALSE) the number of genes corresponding to up and down regulated are compared with those of the reference gene set separately.
默认barplotSignifSignatures执行二项式测试（binom.test包stats）为每个签名最多上调和下调的基因数目是不同的统计学差异。当一个参考基因组提供的测试，如果我们和下调的基因，每个基因组的比例从参考基因组中的比例是不同的。这项工作已经完成，用卡方检验。当参考基因组提供的testUpDown参数TRUE（默认情况下，其FALSE）对应起来，和下调的基因数目与参照基因相比，分别设置， 。
用法----------Usage----------
barplotSignatures(x, signatures, referenceSignature, alpha=.05,
p.adjust.method='none', ylab, cex.text=1, ...)
barplotSignifSignatures(x, signatures, referenceSignature, testUpDown=FALSE,
simulate.p.value = FALSE, B = 10^4, p.adjust.method='none', alpha=.05,
ylab, ylim=ylim, cex.text=1, ...)
参数----------Arguments----------
参数：x
epheno object, as returned by ExpressionPhenoTest.
epheno对象，返回ExpressionPhenoTest的。
参数：signatures
List with each element corresponding to a signature. The gene names in each signature must match those in epheno.
列出每个元素对应一个签名。在每个签名的基因名称必须匹配那些在epheno。
参数：referenceSignature
If specified, the average fold change in each signature is compared to the average fold change in the signature referenceSignature.
如果指定的话，平均每个签名倍倍平均签名referenceSignature的变化进行比较。
参数：testUpDown
If set to TRUE, bars corresponding to up and down-regulated genes are compared with those of referenceSignature separately. This argument is ignored if referenceSignature is not specified.
如果设置为TRUE，条形和下调的基因相比referenceSignature分开。 referenceSignature如果未指定此参数将被忽略。
参数：cex.text
Character expansion for the text indicating the P-values. Ignored if referenceSignature is missing.
表示P值的文本字符扩展。忽略如果referenceSignature丢失。
参数：alpha
Confidence levels for barplot error bars.
为barplot误差棒的信心水平。
参数：p.adjust.method
P-value adjustment method, passed on to p.adjust.
P值调整方法，通过p.adjust。
参数：simulate.p.value
A logical indicating whether chi-square p-values should be computed by Monte Carlo simulation (passed on to chisq.test).
逻辑表示卡方的p值是否应通过蒙特卡罗模拟计算（通过chisq.test）。
参数：B
Integer specifying the number of replicates in the Monte Carlo simulation (passed on to chisq.test).
整数，指定的次数重复在蒙特卡罗模拟（chisq.test）。
参数：ylab
y-axis labels
Y轴标签
参数：ylim
y-axis limits
Y轴限制
参数：...
Other arguments to be passed on to boxplot.
其他参数被传递到盒形图。
值----------Value----------
When a single signature is provided as input, a single plot assessing the association of that signature with all phenotype variables is created. If several signatures are provided, one separate plot is created for each phenotype variable.
当作为输入提供一个单一的签名，评估该签名的关联的所有型变量创建一个单一的图。如果提供了多个签名，创建一个单独的图为每个表型变量。
作者（S）----------Author(s)----------
Evarist Planet
举例----------Examples----------
#create epheno[创建epheno]
data(epheno)
#construct two signatures[建设两个签名]
sign1 <- sample(featureNames(epheno))[1:20]
sign2 <- sample(featureNames(epheno))[1:15]
mySignature <- list(sign1,sign2)
names(mySignature) <- c('My first signature','My preferred signature')
#plot[图]
barplotSignifSignatures(epheno[,'Relapse'],mySignature,alpha=0.05)
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 2012-2-26 11:02:50
