R语言 TEQC包 reads2pairs()函数中文帮助文档(中英文对照)

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reads2pairs(TEQC)
reads2pairs()所属R语言包：TEQC

                                        Merges reads to read pairs
                                         合并读来读对

                                         译者：生物统计家园网 机器人LoveR

描述----------Description----------

Combines the two reads of a read pair (in case of paired-end data) to a new 'range'
结合两读对（配对末端数据的情况下）读取到一个新的“范围”


用法----------Usage----------


reads2pairs(reads, max.distance)



参数----------Arguments----------

参数：reads
RangedData table containing positions of sequenced reads, i.e. output of get.reads. The first 'values' column has to contain read pair identifiers, i.e. when reads was created by get.reads, the option idcol had to be specified. The input can also contain single reads without 'read mate' (e.g. when the first read of a pair did not align to the reference genome, however the second one did align and was still kept). Those single reads will be returned in a separate table singleReads. When the two reads in a pair align to different chromosomes, they will also be returned in table singleReads.
RangedData表，其中包含测序读，即get.reads的输出位置。第一的价值观“一栏中，包含阅读对标识符，即当readsget.reads的创建，选项idcol指定。输入也可以包含单一的读取没有读大副（例如，一对没有对齐的参照基因组的第一次读的时候，但是第二个没有调整，仍然保持）。这些单一的读取将返回一个单独的表singleReads。当两个读在调整不同的染色体配对，他们也将返回表singleReads。


参数：max.distance
Integer value defining the maximum allowed distance between two reads of a pair (from start position of first read to end position of second read). Reads exceeding this distance will be returned in the separate table singleReads. If max.distance is not specified, reads will be joined to pairs regardless of their distance. Only when the two reads in a pair align to different chromosomes, they will be removed in any case and added to table singleReads.
Integer值，定义允许的最大距离两读的一对（从起始位置先读结束的第二次读取的位置）。读取超过这个距离将在单独的表singleReads返回。 max.distance如果不指定，读取将加入对，不管它们之间的距离。只有当两个读在调整不同的染色体配对，他们在任何情况下将被删除，并添加到表singleReads。


Details

详情----------Details----------

The function puts together the two reads of each pair and creates new ranges spanning both reads and everything in between. Those ranges correspond to the extent of the actual DNA molecules for which both ends were sequenced. The output of the function can be used by several other functions, whenever calculations should be based on read pairs rather than on single reads, e.g.
两个每对读取和创建新的范围跨越两个读之间的一切功能放在一起。这些范围符合实际的DNA分子的两端进行测序的程度。其他几项功能，每当计算应读对，而不是基于单输出的功能，可用于读取，如


值----------Value----------

If reads only contains complete read pairs and for all pairs the respective reads align to the same chromosome and their distances do not exceed max.distance (if specified), a RangedData object is returned containing positions of the merged reads per pair, ranging from start position of the first read to end position of the second read.
如果reads只包含完整的阅读对各自的读取所有对对齐到同一染色体的距离不超过max.distance（如果指定），RangedData对象返回包含位置合并后的读取每双不等，从开始的第一次读取的位置，结束第二次读取的位置。

If reads also contains single reads, or if reads within a pair are further apart than max.distance (if specified) or align to different chromosome, a list is returned with elements
如果reads还包含单一的读取，或者如果在一对读取比max.distance（如果指定），或调整到不同的染色体外，将返回一个列表的元素


参数：singleReads
RangedData object containing original positions of single reads without 'read mates' and/or read pairs aligning too far apart or on different chromosomes
RangedData对象，其中包含没有读队友单读取原来的位置和/或对对齐太远或不同的染色体上


参数：readpairs
RangedData object containing positions of the merged reads per pair, ranging from start position of the first read to end position of the second read </table>
RangedData对象包含合并后的位置，读取每双不等，从开始的第一位置读取结束第二次读取的位置</ TABLE>


作者（S）----------Author(s)----------


Manuela Hummel <a href="mailto:manuela.hummel@crg.es">manuela.hummel@crg.es</a>



参见----------See Also----------

get.reads, fraction.reads.target,
get.reads，fraction.reads.target


举例----------Examples----------


exptPath <- system.file("extdata", package="TEQC")
readsfile <- file.path(exptPath, "ExampleSet_Reads.bed")
reads <- get.reads(readsfile, idcol=4, skip=0)
readpairs <- reads2pairs(reads)

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注：
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