compareLists(OrderedList)
compareLists()所属R语言包：OrderedList
Compare Ordered Lists with Weighted Overlap Score
比较分数加权重叠有序列表
译者：生物统计家园网 机器人LoveR
描述----------Description----------
The two orderings received as parameters are compared using the weighted overlap score and compared with a random distribution of that score (yielding an empirical p-value).
作为参数收到的顺序使用加权重叠得分比较，并与随机分布的得分（产生的经验p值）。
用法----------Usage----------
compareLists(ID.List1, ID.List2, mapping = NULL,
two.sided=TRUE, B = 1000, alphas = NULL,
invar.q = 0.5, min.weight = 1e-5,
no.reverse=FALSE)
参数----------Arguments----------
参数：ID.List1
first ordered list of identifiers to be compared.
第一有序标识符列表进行比较。
参数：ID.List2
second ordered list to be compared, must have the same length as ID.List1.
第二个有序列表来进行比较，必须有相同的长度为ID.List1。
参数：mapping
maps identifiers between the two lists. This is a matrix with two columns. All items in ID.List1 must match to exactly one entry of column 1 of the mapping, each element in ID.List2 must match exactly one element in column 2 of the mapping. If mapping is NULL, the two lists are expected to contain the same identifiers and there must be a one-to-one relationship between the two.
这两个列表之间的映射标识符。这是一个具有两列的矩阵。 ID.List1所有项目必须符合完全映射的第1列的一个条目，每个元素ID.List2必须完全匹配一个元素映射的第2栏。如果映射NULL，两个列表包含相同的标识必须是一个一对一的关系，两者之间的。
参数：two.sided
whether the score is to be computed considering both ends of the list, or just the top members.
是否得分是要计算考虑两个名单的两端，或只是顶部的成员。
参数：B
the number of permutations used to estimate empirical p-values.
用于估计经验p值的排列数。
参数：alphas
a set of alpha candidates to be evaluated. If set to NULL, alphas are determined such that reasonable maximal ranks to be considered result.
阿尔法候选人进行评估。如果设置为NULL，阿尔法是决定审议结果的这种合理的最大行列。
参数：invar.q
quantile of genes expected to be invariant. These are not used during shuffling, since they are expected to stay away from the ends of the lists, even when the data is perturbed to generate the NULL distribution. The default of 0.5 is reasonable for whole-genome gene expression analysis, but must be reconsidered when the compared lists are deduced from other sources.
位数的预期是不变的基因。这些都不是在洗牌，因为他们预计到远离名单的两端，甚至当数据扰动生成的NULL分布。 0.5默认为全基因组基因表达分析是合理的，但必须重新考虑从其他来源推断时相比名单。
参数：min.weight
the minimal weight to be considered.
要考虑的最小重量。
参数：no.reverse
skip computing scores for reversed second list.
跳过计算分数反转的第二个列表。
Details
详情----------Details----------
The two lists received as arguments are matched against each other according to the given mapping. The comparison is performed from both ends by default. Permutations of lists are used to generate random scores and compute empirical p-values. The evaluation is also performed for the case the lists should be reversed. From the resulting output, the set of overlapping list identifiers can be extracted using function getOverlap.
收到两个列表作为参数互相匹配，根据给定的映射。默认情况下，从两端进行比较。名单的排列是随机生成的分数和计算经验的p值。名单应扭转的情况下进行的评价。从输出结果，可以提取使用功能getOverlap重叠列表标识符集。
值----------Value----------
An object of class listComparison is returned. It contains the following list elements:
listComparison类的对象被返回。它包含以下列表中的元素：
参数：n
the length of the lists
列表的长度
参数：call
the input parameters
输入参数
参数：nn
the maximal number of genes corresponding to the alphas and the minimal weight
阿尔法相应的基因的最大数和最小重量
参数：scores
scores for the straight list comparisons
分数为直列表比较
参数：revScores
scores for the reversed list comparison
得分逆转的列表比较
参数：pvalues
p-values for the straight list comparison
P-值直列表比较
参数：revPvalues
p-values for the reversed list comparison
P-值的逆转的列表比较
参数：overlap
number of overlapping identifiers per rank in straight comparison
每级的标识符，在直接比较重叠数
参数：revOverlap
number of overlapping identifiers per rank in reversed comparison
数扭转比较重叠，每级的标识符
参数：randomScores
random scores per weighting parameter
每股加权参数的随机分数
参数：ID.List1
same as input ID.List1
与输入ID.List1相同
参数：ID.List2
same as input ID.List2
与输入ID.List2相同
There are print and plot methods for listComparison objects. The plot method takes a parameter which to specify whether "overlap" or "density" is to be drawn.
有listComparison对象的打印和图的方法。图方法需要一个参数which指定“重叠”或“密度”是否要绘制。
作者（S）----------Author(s)----------
Claudio Lottaz, Stefanie Scheid
参考文献----------References----------
参见----------See Also----------
OrderedList, getOverlap
OrderedList，getOverlap
举例----------Examples----------
### Compare two artificial lists with some overlap[＃比较一些重叠的两个人工名单]
data(OL.data)
list1 <- as.character(OL.data$map$prostate)
list2 <- c(sample(list1[1:500]),sample(list1[501:1000]))
x <- compareLists(list1,list2)
x
getOverlap(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。
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 10:15:24
