R语言 OrderedList包 getOverlap()函数中文帮助文档(中英文对照)

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getOverlap(OrderedList)
getOverlap()所属R语言包：OrderedList

                                         Extracting the Intersecting IDs From a listComparison Object
                                         提取从listComparison对象相交的ID

                                         译者：生物统计家园网 机器人LoveR

描述----------Description----------

This function extracts the intersecting set of list identifiers from an object of class listComparison as output of function compareLists. The user has to specify the maximum rank to be considered to receive the intersecting set up to this rank.
这个函数提取从listComparison类的对象的列表标识符集相交作为函数compareLists的输出。用户已被视为收到相交设立这个排名到指定的最高排名。


用法----------Usage----------


getOverlap(x, max.rank = NULL, percent = 0.95)
## S3 method for class 'listComparisonOverlap'
plot(x, which="overlap", no.title=FALSE,  no.legend=FALSE,
     list.name1="List 1", list.name2="List 2", ...)



参数----------Arguments----------

参数：x
An object of class listComparison.  
对象类listComparison。


参数：max.rank
The maximum rank to be considered.  
被视为最大的排名。


参数：percent
The final list of overlapping genes consists of those probes that contribute a certain percentage to the overall similarity score. Default is percent=0.95. To get the full list of genes, set percent=1.  
重叠基因的最终名单，由一定比例的探针，有助于整体的相似性得分。默认percent=0.95。为了获得基因的完整列表，设置percent=1。


参数：which
select what to draw, either 'overlap' or'scores'.
选择要画什么，无论是“重叠”orscores。


参数：no.title
whether to generate a title automatically.
是否自动生成一个标题。


参数：no.legend
whether to generate a legend automatically.
是否自动生成一个传奇。


参数：list.name1
A name for the first list provided to compareLists.
第一个列表的名称compareLists。


参数：list.name2
A name for the second list provided to compareLists.
第二个列表的名称compareLists。


参数：...
Further arguments passed on to generic plot.
进一步的参数传递到通用图。


Details

详情----------Details----------

Function compareLists returns a list comparison for several choices of alpha. The number of genes to be taken into account differs dependent on alpha. One might now want to fix the number of genes and receive the resulting set of intersecting list identifiers. To this end, the user chooses a maximum rank to be considered from the values in column 'Genes' of the listComparison object. The direction (original or reversed) will internally be set to the direction yielding the higher similarity score.
功能compareLists阿尔法几种选择返回一个列表比较。要考虑到不同的基因数目对α依赖。现在可能要修复基因的数量和获得的结果集相交列表标识符。为此，用户选择要考虑从值列基因listComparison对象的最高排名。 （原件或反相）的方向，将在内部设置的方向，产生较高的相似性得分。

If two.sided was TRUE, the first max.rank IDs on top of the lists and the first max.rank identifiers at the end of the lists are considered. If two.sided was FALSE, only the max.rank top identifiers are evaluated for overlap.
如果two.sided是TRUE，第一max.rank上面的名单和第一max.rank名单月底标识符的ID审议。如果two.sided是FALSE，只有max.rank顶部标识符重叠的评价。


值----------Value----------

An object of class listComparisonOverlap is returned. It contains the following list elements:
listComparisonOverlap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 parameters of the input object.
输入对象的参数。


参数：nn
the input max.rank.
的输入max.rank。


参数：score
the observed similarity score.
观测到的相似性得分。


参数：pvalue
p-values for the observed score.
P-值所观察到的得分。


参数：overlaps
number of overlapping identifiers per rank.
数量每级重叠的标识符。


参数：randomScores
random scores for given parameters.
给定参数的随机分数。


参数：direction
numerical value. Returns '1' if the similarity score is higher for the originally ordered lists and '-1' if the score is higher for the comparison of one original to one reversed list.
数值。返回1，如果相似的得分是更高原本有序列表和-1，如果比分是一个比较原始的一个逆转的列表。


参数：intersect
Vector with the sorted overlapping list identifiers, which contribute percent to the overall similarity score.
向量排序重叠的名单标识符，这有助于percent整体的相似性得分。

There are print and plot methods for listComparisonOverlap objects. The plot method takes a parameter which to specify whether "overlap" or "scores" is to be drawn.
有listComparisonOverlap对象的打印和图的方法。图方法需要一个参数which指定是否“重叠”或“分数”要绘制。


作者（S）----------Author(s)----------


Claudio Lottaz, Stefanie Scheid



参考文献----------References----------



参见----------See Also----------

OrderedList, compareLists
OrderedList，compareLists


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：
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