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

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processReads(nucleR)
processReads()所属R语言包：nucleR

                                         Process reads from High-Troughtput Sequencing experiments
                                         从高Troughtput测序实验进程读取

                                         译者：生物统计家园网 机器人LoveR

描述----------Description----------

This method allows the processment of NGS nucleosome reads from different sources and a basic manipulation of them. The tasks includes the correction of strand-specific single-end reads and the trimming of reads to a given length.
这种方法允许，农工商核小体processment从不同的来源和他们的基本操作读取。这些任务包括校正链特异的单端读取和读取给定长度的修剪。


用法----------Usage----------


## S4 method for signature 'AlignedRead'
processReads(data, type = "single", fragmentLen, trim, ...)
## S4 method for signature 'RangedData'
processReads(data, type = "single", fragmentLen, trim, ...)



参数----------Arguments----------

参数：data
Sequence reads objects, probably imported using other packages as ShortRead.        Allowed object types are AlignedRead and RangedData with a strand attribute.  
序列读取对象，可能使用其他包ShortRead进口。允许对象类型是AlignedRead和RangedDatastrand属性。


参数：type
Describes the type of reads. Values allowed are single for single-ended reads and paired for paired-ended.  
介绍了读取的类型。允许的值是single单端读取和paired配对结束。


参数：fragmentLen
Expected original length of the sequenced fragments. See details.          
预计的原始长度的序列片段。查看详情。


参数：trim
Length to trim the reads (or extend them if trim > read length)  
长度修剪的读取（或延长他们如果trim>读取长度）


参数：...
Other parameters passed to fragmentLenDetect if no fixed fragmentLen is given.  
其他参数传递给如果没有固定的fragmentLenDetect fragmentLen。


Details

详情----------Details----------

This function reads a AlignedRead or a RangedData object containing the position, length and strand of the sequence reads.
该函数读取AlignedRead或RangedData对象包含的位置，长度和链序列读取。

It allows the processment of both paired and single ended reads. In the case of single end reads this function corrects the strand-specific mapping by shifting plus strand reads and minus strand reads towards a middle position where both strands are overlaped. This is done by accounting the expected fragment length (fragmentLen).
它允许成对和单端processment读取。在单端的情况下读取此功能，纠正转向中间位置，两股是overlaped加股读取和负链读取钢绞线特定的映射。这是由会计的预期片段长度（fragmentLen）。

For paired end reads, mononucleosomal reads could extend more than expected length due to mapping issues or experimental conditions. In this case, the fragmentLen variable sets the threshold from which reads longer than it should be ignored.
为配对年底读取，mononucleosomal的的读取可以延长超过映射问题或实验条件下，由于预期长度。在这种情况下，fragmentLen变量设置的阈值，从其中读取的时间比它应该被忽略。

If no value is supplied for fragmentLen it will be calculated automatically (increasing the computing time) using fragmentLenDetect with default parameters. Performance can be increased by tunning fragmentLenDetect parameteres in a separated call and passing its result as fragmentLen parameter.
如果没有提供值fragmentLen它会被自动计算（增加了计算时间）fragmentLenDetect默认参数。 tunning在一个分离的呼叫fragmentLenDetect的parameteres和传递fragmentLen参数，其结果可提高性能。

In some cases, could be useful trim the reads to a shorter length to improve the detection of nucleosome dyads, easing its detection and automatic positioning. The parameter trim allows the selection of how many nucleotides select from each read.
在某些情况下，可能是有用的修剪读取较短的长度，以提高检测的核小体的二元关系，缓和其检测和自动定位。参数trim允许读取的选择，每个选择多少个核苷酸。

A special case for single-ended data is setting the trim to the same value as fragmentLen, so the reads will be extended strand-wise towards the 3' direction, creating an artificial map comparable with paired-ended data. The same but opposite can be performed with paired-end data, setting a trim value equal to the read length from paired ended, so paired-ended data will look like single-ended..
单端数据的一个特殊情况设置trim到fragmentLen值相同，所以读取将延长链明智向3方向，创造一个人工配对相媲美图截至数据。相同但方向相反，可以进行配对末端数据，设置trim配对结束读取的长度等于价值，所以配对结束数据将像单端..


值----------Value----------

RangedData containing the aligned/trimmed individual reads
RangedData包含对齐/修剪个别读


注意----------Note----------

<STRONG>IMPORTANT</STRONG>: this information is only used to correct possible strand-specific mapping, this package doesn't link the two ends of paired reads.
<STRONG>重要</ strong>：此信息仅用于纠正可能出现的链特定的映射，这个包不连接两端配对读取。


作者（S）----------Author(s)----------



Oscar Flores <a href="mailtoflores@mmb.pcb.ub.es">oflores@mmb.pcb.ub.es</a>




参见----------See Also----------

AlignedRead, RangedData, fragmentLenDetect
AlignedRead，RangedData，fragmentLenDetect


举例----------Examples----------


       
        #Load data        [加载数据]
        data(nucleosome_htseq)
       
        #Process nucleosome reads, select only those shorter than 200bp[读取过程中核小体，只选择那些短比200bp]
        pr1 = processReads(nucleosome_htseq, fragmentLen=200)
       
        #Now process them, but picking only the 40 bases surrounding the dyad[现在处理这些，但只有40个碱基周边的对子采摘]
        pr2 = processReads(nucleosome_htseq, fragmentLen=200, trim=40)

        #Compare the results:[比较结果：]
        par(mfrow=c(2,1), mar=c(3,4,1,1))
        plot(as.vector(coverage(pr1)[["chr1"]]), type="l", ylab="coverage (original)")
        plot(as.vector(coverage(pr2)[["chr1"]]), type="l", ylab="coverage (trimmed)")



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