enrichedPeaks(htSeqTools)
enrichedPeaks()所属R语言包：htSeqTools
Find peaks in sequencing experiments.
测序实验中发现峰。
译者：生物统计家园网 机器人LoveR
描述----------Description----------
Find peaks in significantly enriched regions found via enrichedRegions.
查找峰通过enrichedRegions发现显着富集的区域。
用法----------Usage----------
enrichedPeaks(regions, sample1, sample2, minHeight=100, space, mc.cores=1)
参数----------Arguments----------
参数：regions
RangedDataList or RangedData indicating the regions in which we wish to find peaks.
RangedDataList或RangedData指示中，我们希望能找到峰区域。
参数：sample1
IRangesList or IRanges object containing start and end of sequences in sample 1.
IRangesList或IRanges对象包含在样品1序列的开始和结束。
参数：sample2
Same for sample 2. May be left missing, in which case only sample1 is used to find peaks.
样品2相同。可留丢失，在这种情况下，只有sample1是用来寻找峰。
参数：minHeight
If sample2 is missing, peaks are defined as regions where the coverage in sample1 is greater or equal than minHeight. If sample2 is specified, the difference of coverage in sample1 minus sample2 must be greater or equal than minHeight.
sample2如果缺少峰被定义为区域覆盖sample1大于等于或比minHeight。如果sample2指定，覆盖在SAMPLE1减去的sample2差异必须大于或比minHeight平等。
参数：space
Character text giving the name of the space for the RangedData object. Only used if sample1 and sample2 are of class RangedData, for RangedDataList this is set up automatically.
字符的文本给予空间RangedData对象的名称。只有使用sample1和sample2类RangedData，RangedDataList这是自动成立。
参数：mc.cores
If mc.cores>1 computations for each element in the IRangesList objects are performed in parallel (using the parallel function from package multicore). Notice: this option launches as many parallel processes as there are elements in x, which can place strong demands on the processor and memory.
如果mc.cores> 1计算每个元素在IRangesList对象的并行执行（包parallelmulticore函数）。注意：此选项，因为许多并行进程启动有x，它可以将强烈要求对处理器和内存中的元素。
值----------Value----------
Object of class RangedData indicating peaks higher than minHeight. Only peaks overlapping with regions are reported. The maximum of the coverage in each selected peak is reported in the column height (coverage in sample1 - sample2 when sample2 is specified). The column region.pvalue returns the p-value associated to the region that the peak belongs to (i.e. it is inherited from regions). Therefore, notice that all peaks corresponding to a single region will present the same region.pvalue.
对象类RangedData比minHeight表明峰更高。只有以regions重叠峰报告。据报道，在柱的高度（覆盖SAMPLE1 - 的sample2指定的sample2时）最大覆盖在每个选定的高峰。列region.pvalue返回的p值与该区域相关的峰值（即它是从regions继承）。因此，发现所有的峰对应到一个单一的区域将呈现相同的region.pvalue。
方法----------Methods----------
sample2 = "IRanges")</dt> sample1 indicates the start/end of reads in sample 1, and similarly for sample2. Only the subset of
的sample2 =“IRanges）</代码> </ DT>sample1表示读取样品1开始/结束，同样sample2。只有子集
signature(regions = "RangedData", sample1 = "IRanges", sample2 = "missing") sample1 indicates the start/end of reads in sample 1, and similarly for sample2. Only the subset of
signature(regions = "RangedData", sample1 = "IRanges", sample2 = "missing")sample1表示读取样品1开始/结束，同样sample2。只有子集
sample2 = "IRangesList")</dt> regions contains the regions of interest, sample1 and sample2 the reads in sample 1 and sample 2, respectively. names(sample1) and
的sample2 =“IRangesList）</代码> </ DT>regions包含感兴趣的区域，sample1和sample2读取，分别在样品1和样品2。 names(sample1)“
signature(regions = "RangedData", sample1 = "IRangesList", sample2 = "missing") regions contains the regions of interest, sample1 the reads in sample 1.
signature(regions = "RangedData", sample1 = "IRangesList", sample2 = "missing")regions包含感兴趣的区域，sample1样品1读取。
sample2 = "missing")</dt> space(sample1) indicates the chromosome, and start(sample1) and
的sample2 =“失踪”）</代码> </ DT>space(sample1)表示染色体，start(sample1)“
signature(regions = "RangedData", sample1 = "RangedData", sample2 = "RangedData") space(sample1) indicates the chromosome, and start(sample1) and end(sample1) indicate the start/end of the reads in sample 1.
signature(regions = "RangedData", sample1 = "RangedData", sample2 = "RangedData")space(sample1)表示染色体，和start(sample1)和end(sample1)表明读取样品1开始/结束。
参见----------See Also----------
enrichedRegions
enrichedRegions
举例----------Examples----------
set.seed(1)
st <- round(rnorm(1000,500,100))
strand <- rep(c('+','-'),each=500)
space <- rep('chr1',length(st))
sample1 <- RangedData(IRanges(st,st+38),strand=strand,space=space)
st <- round(runif(1000,1,1000))
sample2 <- RangedData(IRanges(st,st+38),strand=strand,space=space)
#Find enriched regions and call peaks[找到丰富的区域，并呼吁峰]
mappedreads <- c(sample1=nrow(sample1),sample2=nrow(sample2))
regions <- enrichedRegions(sample1,sample2,mappedreads=mappedreads,minReads=50)
peaks <- enrichedPeaks(regions,sample1=sample1,sample2=sample2,minHeight=50)
peaks <- peaks[width(peaks)>10,]
peaks
#Compute coverage in peaks[在峰值计算覆盖率]
cover <- coverage(sample1)
coverinpeaks <- regionsCoverage(chr=space(peaks),start=start(peaks),end=end(peaks),cover=cover)
#Evaluate coverage in regular grid and plot[评估覆盖在常规电网和图]
#Can be helpful fo clustering of peak profiles[可以有助于高峰型材FO聚类]
coveringrid <- gridCoverage(coverinpeaks)
coveringrid
plot(coveringrid)
#Standardize peak profiles dividing by max coverage[规范除以最大覆盖高峰型材]
stdcoveringrid <- stdGrid(coveringrid, colname='maxCov')
stdcoveringrid
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注：
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发表于 2012-2-25 22:02:10
