findOverlaps(oligoClasses)
findOverlaps()所属R语言包：oligoClasses
Find markers that overlap with a query set of ranges
查找与查询集的范围重叠的标记
译者：生物统计家园网 机器人LoveR
描述----------Description----------
Methods for finding overlapping genomic ranges.
重叠的基因组范围内寻找方法。
用法----------Usage----------
findOverlaps(query, subject, maxgap = 0L, minoverlap = 1L, type = c("any", "start", "end", "within", "equal"), select = c("all", "first", "last", "arbitrary"), ...)
参数----------Arguments----------
参数：query
A RangedDataCNV object.
一个RangedDataCNV对象。
参数：subject
A SnpSet, a CNSet or the featureData from these classes. The featureData must be an AnnotatedDataFrame.
一个SnpSet，CNSet或featureData从这些类。 featureData必须是一个AnnotatedDataFrame。
参数：maxgap
Passed to findOverlaps method for a IRanges query and a IRanges subject.
通过findOverlapsIRanges查询IRanges主题的方法。
参数：minoverlap
Passed to findOverlaps method for a IRanges query and a IRanges subject.
通过findOverlapsIRanges查询IRanges主题的方法。
参数：type
Passed to findOverlaps method for a IRanges query and a IRanges subject.
通过findOverlapsIRanges查询IRanges主题的方法。
参数：select
Passed to findOverlaps method for a IRanges query and a IRanges subject.
通过findOverlapsIRanges查询IRanges主题的方法。
参数：...
Passed to findOverlaps method for a IRanges query and a IRanges subject.
通过findOverlapsIRanges查询IRanges主题的方法。
Details
详情----------Details----------
When both query and subject are RangedDataCNV objects, we require that the overlapping ranges have the same chromosome and sample id. If query and subject are RangedDataHMM objects we additionally require that the state value in the RangedDataHMM objects match. For example, if the same genomic interval for a subject is called a 'deletion' in query and 'normal' in subject, the interval is not matched. The primary purpose of such queries is to assess the concordance of hidden Markov models applied to the same dataset.
当两个query和subject是RangedDataCNV对象，我们需要重叠的范围，具有相同的染色体和样品编号。如果query和subject是RangedDataHMM对象，我们另外需要state对象匹配的价值RangedDataHMM。例如，如果一个主题相同的基因组间隔被称为“删除”query和正常subject，间隔不匹配。这样的质疑的主要目的是评估的隐马尔可夫模型应用到相同的数据集的一致性。
If subject is a SnpSet, CNSet, or AnnotatedDataFrame with 'chromosome', and 'position' varLabels, the method returns a RangesMatching object indicating which markers in subject overlap with the query ranges. This method can be useful for finding the set of markers in subject that reside within a given genomic interval in the query.
subject如果是SnpSet，CNSet或AnnotatedDataFrame与染色体，位置varLabels，该方法返回一个RangesMatching对象显示在标记subjectquery范围重叠。这种方法可以找到一套标记subject驻留在一个给定的基因组间隔query。
值----------Value----------
A RangesMatching object.
一个RangesMatching对象。
作者（S）----------Author(s)----------
R. Scharpf
举例----------Examples----------
if(require("VanillaICE")){
data(hmmResults, package="VanillaICE")
data(oligoSetExample)
## Find markers in a oligoSnpSet object that overlap with the[＃查找在oligoSnpSet对象标记与重叠。]
## 2nd range:[＃第二个范围：]
rmatching <- findOverlaps(hmmResults[2, ], oligoSet)
index.in.range <- matchMatrix(rmatching)[,2]
features.in.range <- featureNames(oligoSet)[index.in.range]
##[＃]
## For two RangedDataHMM objects, returns only the ranges[＃两年RangedDataHMM对象，只返回的范围]
## that have the same sample name, chromosome, and HMM state[＃有相同的样品名称，染色体，HMM状态]
## A trivial example:[＃一个简单的例子：]
hmmResults2 <- hmmResults
hmmResults2$state <- rep(3, nrow(hmmResults))
findOverlaps(hmmResults, hmmResults2)
}
转载请注明:出自 生物统计家园网(http://www.biostatistic.net)。
注：
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发表于 2012-2-26 08:07:28
