alignPeaks(htSeqTools)
alignPeaks()所属R语言包：htSeqTools
Align peaks in a ChIP-Seq experiment by removing the strand
通过消除铸坯对齐峰在一个芯片SEQ实验
译者：生物统计家园网 机器人LoveR
描述----------Description----------
Align peaks in a ChIP-Seq experiment by removing the shift between reads aligned to the plus and the minus strands.
消除之间的加号和减号股对齐读取的转变对齐峰在一个芯片SEQ实验。
用法----------Usage----------
alignPeaks(x, strand, npeaks = 1000, bandwidth = 150, mc.cores=1)
参数----------Arguments----------
参数：x
A RangedDataList, RangedData or an IRangesList object containing the aligned reads in each chromosome.
ARangedDataList，RangedData或IRangesList对齐对象，其中包含在每个染色体读取。
参数：strand
Strand that each read was aligned to. If x is of class RangedDataList, strand can be a character vector of length 1 indicating the name of the field in x indicating the strand, i.e. x[[1]][[strand]] contains the strand information.
东街，每读对齐。 x如果类RangedDataList，strand可以是一个长度为1的特征向量表明领域x表示链，即x[[1]][[strand]]的名称包含链信息。
参数：npeaks
Number of peaks to be used to estimate the shift size.
数被用来估计移位的大小山峰。
参数：bandwidth
Only reads with distance less than bandwidth between them and their closest gene are used to estimate the shift size.
只读取距离比bandwidth他们和他们最接近的基因被用来估计移位大小。
参数：mc.cores
Number of cores to be used for parallel computing (passed on to mclapply). Only used if x is of class RangedDataList.
用于并行计算的核心数量（通过mclapply）。只用了如果x类RangedDataList。
Details
详情----------Details----------
The procedure detects the npeaks highest peaks (using reads from both strands simultaneously). Then it selects reads which are less than bandwidth base pairs away from any of the peaks. Then it computes (a) the average distance between reads on the plus strand and the closest peak, (b) the same distance for reads on the minus strand. The mean difference between (a) and (b) is the estimated shift size. Reads on the plus strand are shifted to the right, whereas reads on the minus strands are shifted to the left.
过程检测npeaks最高的山峰（使用从两股同时读取）。然后选择读取不到bandwidth碱基对，离峰任何。然后计算（一）之间的平均距离读取加链和最接近的高峰期，（二）同一距离的负链上读取。平均差之间的（a）及（b）是估计移大小。读取上加上链向右移，而负链上读取左移。
值----------Value----------
A CompressedIRangesList object with all reads shifted so that the strand specific bias is no longer present.
一个CompressedIRangesList转移链特定的偏见，使不再是目前所有读取的对象。
方法----------Methods----------
signature(x = "IRangesList", strand = "list") Each element in x corresponds to a chromosome, and each range gives the start/end of a sequence. strand indicates the strand for
signature(x = "IRangesList", strand = "list")x的每个元素对应一个染色体，每个范围给出了序列的开始/结束。“ strand表示链
x gives read start and end positions, and strand gives
x使阅读开始和结束位置，strand给
The method for RangedData is applied to each element in x separately, as each element may
的方法RangedData“被应用到每个元素x分别为每个元素，可
举例----------Examples----------
#Generate 1000 reads containing strand-specific bias[生成1000读取含有特定链偏见]
st <- runif(1000,1,250)
strand <- rep(c('+','-'),each=500)
st[strand=='-'] <- st[strand=='-'] + runif(500,50,100)
x <- RangedData(IRanges(st,st+38),strand=strand)
#Estimate and remove the bias[估计和消除偏见]
xalign <- alignPeaks(x, strand='strand', npeaks=1)
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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 22:00:53
