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

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peaksNearBDP(ChIPpeakAnno)
peaksNearBDP()所属R语言包：ChIPpeakAnno

                                         obtain the peaks near bi-directional promoters
                                         获得双向启动子附近的峰

                                         译者：生物统计家园网 机器人LoveR

描述----------Description----------

Obtain the peaks near bi-directional promoters. Also output percent of peaks near bi-directional promoters.
获得双向启动子附近的山峰。双向启动子附近的山峰也输出％。


用法----------Usage----------


peaksNearBDP(myPeakList, mart,AnnotationData, MaxDistance=5000,PeakLocForDistance = c("start", "middle", "end"),
FeatureLocForDistance = c("TSS", "middle","start", "end","geneEnd"))



参数----------Arguments----------

参数：myPeakList
RangedData: See example below
RangedData：参见下面的例子


参数：mart
used if AnnotationData not supplied, a mart object, see useMart of bioMaRt package for details  
使用如果AnnotationData不提供，集市对象，详见bioMaRt包useMart，


参数：AnnotationData
annotation data obtained from getAnnotation or customized annotation of class RangedData containing additional variable:  strand (1 or + for plus strand and -1 or - for minus strand). For example, data(TSS.human.NCBI36),data(TSS.mouse.NCBIM37), data(TSS.rat.RGSC3.4) and data(TSS.zebrafish.Zv8) . If not supplied, then annotation will be obtained from biomaRt automatically using the parameters of mart and featureType TSS
注释类RangedData包含额外的变量从getAnnotation或定制的注释得到的数据：股（1加链和-1或+或 - 负链）。例如，数据（TSS.human.NCBI36），数据（TSS.mouse.NCBIM37），数据（TSS.rat.RGSC3.4）和数据（TSS.zebrafish.Zv8）。如果没有提供，那么注释将从biomaRt获得使用TSS的集市和featureType的的参数，自动


参数：MaxDistance
Specify the maximum gap allowed between the peak and nearest gene
指定高峰和最近的基因之间允许的最大差距


参数：PeakLocForDistance
Specify the location of peak for calculating distance,i.e., middle means using middle of the peak to calculate distance to feature, start means using start of the peak to calculate the distance to feature. To be compatible with previous version, by default using start
指定的峰值计算距离的位置，即中间是指使用中间的高峰期，以功能来计算距离，开始使用的高峰期开始计算距离功能。为了与以前的版本兼容，默认情况下使用开始


参数：FeatureLocForDistance
Specify the location of feature for calculating distance,i.e., middle means using middle of the feature to calculate distance of peak to feature, start means using start of the feature to calculate the distance to feature, TSS means using start of feature when feature is on plus strand and using end of feature when feature is on minus strand, geneEnd means using end of feature when feature is on plus strand and using start of feature when feature is on minus strand. To be compatible with previous version, by default using TSS
指定的功能计算距离的位置，即中间意味着使用功能的中间计算距离峰值功能，启动意味着使用功能开始计算距离功能，可溶性固形物是指开始时的特点是使用功能加链和使用功能是负链上的功能结束时，geneEnd意味着使用功能结束时功能，加上股和功能是负链时使用的功能开始。为了与以前的版本兼容，默认使用TSS


值----------Value----------

A list of 4
4名单


参数：<code>peaksWithBDP</code>
annotated Peaks containing bi-directional promoters.  RangedData with slot start holding the start position of the peak, slot end holding the end position of the peak, slot space holding the chromosome location where the peak is located, slot rownames holding the id of the peak. In addition, the following variables are included.  feature: id of the feature such as ensembl gene ID  insideFeature: upstream: peak resides upstream of the feature; downstream: peak resides downstream of the feature; inside: peak resides inside the feature; overlapStart: peak overlaps with the start of the feature; overlapEnd: peak overlaps with the end of the feature; includeFeature: peak include the feature entirely.  distancetoFeature: distance to the nearest feature such as transcription start site.  By default, the distance is calculated as the distance between the start of the binding site and the TSS that is the gene start for genes located on the forward strand and the gene end for genes located on the reverse strand. The user can specify the location of peak and location of feature for calculating this  start_position: start position of the feature such as gene  end_position: end position of the feature such as the gene  strand: 1 or + for positive strand and -1 or - for negative strand where the feature is located  shortestDistance: The shortest distance from either end of peak to either end the feature  fromOverlappingOrNearest: NearestStart: indicates this PeakLocForDistance is closest to the  FeatureLocForDistance  
含有注明双向启动子峰。与插槽RangedData开始举行的高峰期的开始位置，槽年底举行的高峰期的结束位置，槽空间峰位于染色体上的位置，峰的ID的的插槽rownames控股。此外，包括下列变量。功能：ID的，如ENSEMBL基因身份证insideFeature特征：上游：高峰上游所在的功能;下游：高峰下游驻留功能;内：高峰内的功能所在; overlapStart：高峰重叠与功能开始;包括功能完全overlapEnd：高峰重叠与功能; includeFeature：峰值。 distancetoFeature：距离最近的功能，如转录起始位点。默认情况下，距离计算的结合位点的启动和TSS的是基因的基因位于正向链和反向链上的基因位于基因年底开始之间的距离。用户可以指定峰值的位置计算这个start_position和功能的位置：起始位置的功能，如基因end_position：年底的功能，如基因链的位置：正股和-1 1或+或 - 负链功能位于shortestDistance：最短距离，无论从高峰期的结束任一端功能fromOverlappingOrNearest：，NearestStart：表示最接近的FeatureLocForDistance的这个PeakLocForDistance是


参数：<code>percentPeaksWithBDP</code>
The percent of input peaks containing bi-directional promoters
％输入含有双向启动子峰


参数：<code>n.peaks</code>
The total number of input peaks
输入峰的总数


参数：<code>n.peaksWithBDP</code>
The # of input peaks containing bi-directional promoters
输入含有双向启动子峰＃


作者（S）----------Author(s)----------


Lihua Julie Zhu



参考文献----------References----------

<h3>See Also</h3>

举例----------Examples----------



if (interactive())
{
        data(myPeakList)
        data(TSS.human.NCBI36)
        annotatedBDP = peaksNearBDP(myPeakList[1:6,], AnnotationData=TSS.human.NCBI36,
        MaxDistance=5000,PeakLocForDistance =  "middle",
        FeatureLocForDistance = "TSS")
        c(annotatedBDP$percentPeaksWithBDP, annotatedBDP$n.peaks, annotatedBDP$n.peaksWithBDP)
}

转载请注明:出自 生物统计家园网(http://www.biostatistic.net)。


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