findOverlappingPeaks(ChIPpeakAnno)
findOverlappingPeaks()所属R语言包：ChIPpeakAnno
Find the overlapping peaks for two peak ranges.
找到两个峰值范围叠嶂。
译者：生物统计家园网 机器人LoveR
描述----------Description----------
Find the overlapping peaks for two input peak ranges.
寻找两个输入峰值范围叠嶂。
用法----------Usage----------
findOverlappingPeaks(Peaks1, Peaks2, maxgap = 100, multiple = c(TRUE, FALSE),
NameOfPeaks1 = "TF1", NameOfPeaks2 = "TF2",
select=c("all", "first","last","arbitrary"))
参数----------Arguments----------
参数：Peaks1
RangedData: See example below.
RangedData：参见下面的例子。
参数：Peaks2
RangedData: See example below.
RangedData：参见下面的例子。
参数：maxgap
Non-negative integer. Intervals with a separation of maxgap or less are considered to be overlapping.
非负整数。考虑重叠分离的maxgap或更少的时间间隔。
参数：multiple
TRUE or FALSE: TRUE may return multiple overlapping peaks in Peaks2 for one peak in Peaks1; FALSE will return at most one overlapping peaks in Peaks2 for one peak in Peaks1. This parameter is kept for backward compatibility, please use select.
TRUE或FALSE TRUE可能返回一个在Peaks1高峰多个重叠在Peaks2峰，FALSE将返回一个一个在Peaks1高峰重叠在Peaks2峰。此参数为保持向后兼容性，请选择。
参数：NameOfPeaks1
Name of the Peaks1, used for generating column name.
用于生成列名的Peaks1，名称。
参数：NameOfPeaks2
Name of the Peaks2, used for generating column name.
用于生成列名的Peaks2，名称。
参数：select
all may return multiple overlapping peaks, first will return the first overlapping peak, last will return the last overlapping peak and arbitrary will return one of the overlapping peaks.
所有可能返回多个叠嶂，首先将返回第一个重叠的高峰，最后会回到过去的重叠峰，并任意将返回叠嶂之一。
Details
详情----------Details----------
Efficiently perform overlap queries with an interval tree implemented in IRanges.
有效地执行与实施的时间间隔在IRanges树重叠的查询。
值----------Value----------
参数：OverlappingPeaks
a data frame consists of input peaks information with added information: overlapFeature (upstream: peak1 resides upstream of the peak2; downstream: peak1 resides downstream of the peak2; inside: peak1 resides inside the peak2 entirely; overlapStart: peak1 overlaps with the start of the peak2; overlapEnd: peak1 overlaps with the end of the peak2; includeFeature: peak1 include the peak2 entirely) and shortestDistance (shortest distance between the overlapping peaks)
一个数据框由输入峰的信息，补充信息：overlapFeature（上游：驻留peak1上游的peak2的;下游：下游peak1所在的peak2;内部：内peak2完全peak1所在; overlapStart：peak1开始重叠peak2; overlapEnd：peak1重叠年底的peak2; includeFeature：peak1包括完全的peak2）和shortestDistance（叠嶂之间最短的距离）
参数：MergedPeaks
RangedData contains merged overlapping peaks
RangedData包含合并叠嶂
作者（S）----------Author(s)----------
Lihua Julie Zhu
参考文献----------References----------
2.Zhu L.J. et al. (2010) ChIPpeakAnno: a Bioconductor package to annotate ChIP-seq and ChIP-chip data. BMC Bioinformatics 2010, 11:237doi:10.1186/1471-2105-11-237
参见----------See Also----------
annotatePeakInBatch, makeVennDiagram
annotatePeakInBatch，makeVennDiagram
举例----------Examples----------
if (interactive())
{
peaks1 = RangedData(IRanges(start=c(1543200,1557200,1563000,1569800,167889600),
end=c(1555199,1560599,1565199,1573799,167893599),names=c("p1","p2","p3","p4","p5")),
strand=as.integer(1),space=c(6,6,6,6,5))
peaks2 = RangedData(IRanges(start=c(1549800,1554400,1565000,1569400,167888600),
end=c(1550599,1560799,1565399,1571199,167888999),names=c("f1","f2","f3","f4","f5")),
strand=as.integer(1),space=c(6,6,6,6,5))
t1 =findOverlappingPeaks(peaks1, peaks2, maxgap=1000,
NameOfPeaks1="TF1", NameOfPeaks2="TF2", select="all")
r = t1$OverlappingPeaks
pie(table(r$overlapFeature))
as.data.frame(t1$MergedPeaks)
}
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 14:48:27
