listOverlap(htSeqTools)
listOverlap()所属R语言包：htSeqTools
Assess the overlap between two or three lists.
评估两个或三个列表之间的重叠。
译者：生物统计家园网 机器人LoveR
描述----------Description----------
Assess the overlap between two or three lists, e.g. ChIP-Seq peaks vs. genes selected from a microarray, or peaks obtained in different experiments.
评估两个或三个列表之间的重叠，如从芯片的SEQ峰与基因芯片，或在不同的实验中获得的高峰。
用法----------Usage----------
listOverlap(list1, list2, list3, univ, ...)
参数----------Arguments----------
参数：list1
Vector with elements in the first list. This can either be a character vector indicating the element names, or a named factor vector indicating some classification for the elements in the first list.
向量的第一个列表中的元素。这可以是一个字符向量表示的元素名称，或一个名为因素向量，说明一些在第一个列表的元素进行分类。
参数：list2
Vector with elements in the second list. This should be a character vector indicating the element names.
第二个列表中的元素的向量。这应该是一个特征向量表示的元素名称。
参数：list3
Vector with elements in the third list. This should be a character vector indicating the element names. The overlap assesment method used depends on whether this argument is specified or not. See details.
第三个列表中的元素的向量。这应该是一个特征向量表示的元素名称。重叠使用的评定方法取决于是否指定或没有这种说法。查看详情。
参数：univ
character vector indicating the universe of all elements from which list1 and list2 were obtained. The overlap assessment depends on whether this argument is specified or not. See details.
特征向量表示从list1和list2得到的所有元素的宇宙。重叠评估取决于是否指定或没有这种说法。查看详情。
参数：...
Further arguments to be passed on to chisq.test in 2 list overlapping.
进一步传递参数给chisq.test2名单重叠。
Details
详情----------Details----------
For signature(list1='character', list2='character', list3='missing', univ='character') the overlap is assessed with respect to the universe of all possible elements univ. That is, we count the number of elements that are common to list1 and list2, those appearing only in either list1 or list2, and those not appearing in either (but appearing in univ). A typical example: list1 contains names of genes with a peak in ChIP-Seq experiment 1, list2 names of genes with a peak in ChIP-Seq experiment 2, and univ the names of all genes in the organism.
签字（list1的=“字符”，列表2 =字符，项目list3 =失踪，大学=字符）评估与宇宙中所有可能的元素重叠univ。也就是说，我们算list1和list2是共同的元素，那些只出现在列表1或列表2，那些没有出现在任何（但出现在univ）。一个典型的例子：list1包含在基因芯片SEQ实验1list2名称基因芯片序列实验2的高峰，和univ名峰名在所有生物体的基因。
For signature(list1='character', list2='character', list='character', univ='character') the overlap is assessed by fitting and anova comparison of linear models. This is done to test whether 3-way overlap is significant with respect to the universe of all possible elements univ when compared to a model considering just the combination of 2-way overlapping. A typical example: list1, list2 and list3 contain names of genes with peaks in three different ChIP-Seq experiments, and univ the names of all genes in the organism.
对于签名（list1的“字符”，列表2 =“字符”，列表=字符，大学=字符）重叠线性模型的拟合和方差比较评估。这样做是为了测试3路重叠是否是宇宙中所有可能的元素方面具有重要意义univ时相比，只考虑2路重叠组合模型。一个典型的例子：list1，list2和list3基因的名称，并包含三种不同的芯片SEQ实验峰univ生物体中所有基因的名称。
For signature(list1='factor', list2='character', univ='missing') the distribution of list1 is compared between elements appearing and not appearing in list2. A typical example: list1 indicates the differential expression status for a number of genes, and list2 contains the names of the genes which had a peak in a ChIP-Seq experiment.
对于签名（列表1 =因素，列表2 =字符=失踪）的分布大学list1比之间出现的元素，而不是出现在list2。一个典型的例子：list1表明基因差异表达的状态，和list2包含的基因，其中有一个高峰在一个芯片SEQ实验的名称。
值----------Value----------
For comparison of 2 lists, an htest object from a chi-square test that evaluates if the two lists are statistically independent from each other. This is a named list: the observed overlap is stored in observed and the P-value in p.value.
2列出作比较，htest从卡方检验，评估，如果这两个列表统计是相互独立的对象。这是一个名为名单：观察重叠存储在observed在p.valueP值。
For 3 list comparison, a list object containing the occurrence and frequency tables (xtab, ftable), the fitted linear models (glm1, glm2), and the anova P-value (pvalue).
比较列表3，list对象，其中包含的发生和频率表（xtab，ftable），拟合线性模型（glm1，glm2） ANOVA P值（pvalue）。
方法----------Methods----------
signature(list1 = "character", list2 = "character", list3 = "character", univ = "character") Studies 3-way associations.
signature(list1 = "character", list2 = "character", list3 = "character", univ = "character")研究3路协会。
signature(list1 = "character", list2 = "character", list3 = "missing", univ = "character") Studies bivariate associations.
signature(list1 = "character", list2 = "character", list3 = "missing", univ = "character")研究二元协会。
signature(list1 = "factor", list2 = "character", list3 = "missing", univ = "missing") Studies bivariate associations.
signature(list1 = "factor", list2 = "character", list3 = "missing", univ = "missing")研究二元协会。
举例----------Examples----------
#Overlap between diff expression and chip-seq peaks[差异表达芯片SEQ峰之间的重叠]
deStatus <- factor(c(0,0,0,0,1,1,1))
names(deStatus) <- paste('Gene',1:7)
peaks <- c('Gene 6','Gene 7')
ans <- listOverlap(list1=deStatus,list2=peaks)
ans$observed
ans$p.value
#Overlap between peaks obtained from two different experiments[从两个不同的实验获得峰之间的重叠]
peaks2 <- c('Gene 1','Gene 2','Gene 7')
univ <- paste('Gene',1:7)
ans <- listOverlap(list1=peaks,list2=peaks2,univ=univ)
ans$observed
ans$p.value
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 2012-2-25 22:03:50
