R语言 TEQC包 fraction.reads.target()函数中文帮助文档(中英文对照)

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fraction.reads.target(TEQC)
fraction.reads.target()所属R语言包：TEQC

                                        Target capture specificity
                                         目标捕获特异性

                                         译者：生物统计家园网 机器人LoveR

描述----------Description----------

Calculates the fraction of reads that align to target regions.
计算读取的部分，对准目标区域。


用法----------Usage----------


fraction.reads.target(reads, targets, Offset = 0, mappingReads = FALSE)



参数----------Arguments----------

参数：reads
RangedData table containing positions of sequenced reads, i.e. output of get.reads. Alternatively, for paired-end data, it can be the output of reads2pairs when fraction of on-target read pairs shall be calculated instead of fraction of single on-target reads.
RangedData表，其中包含测序读，即get.reads的输出位置。另外，配对末端数据，它可以输出reads2pairs靶上的分数时，读双应，而不是单一的分数目标如下计算。


参数：targets
RangedData table containing positions of target regions, i.e. output from get.targets
RangedData表，其中包含目标区域的位置，即从get.targets输出


参数：Offset
integer; add Offset bases on both sides to targeted regions and potentially collapse resulting overlapping target regions
整数;加上Offset双方针对区域的碱基和潜在的崩溃导致重叠的目标区域


参数：mappingReads
if TRUE, reduced RangedData table with only those reads mapping to target regions is returned. When reads is output of reads2pairs, mappingReads will be the corresponding subset of on-target read pairs.
如果只有那些读取映射到目标区域的TRUE，减少RangedData表返回。当readsreads2pairs的输出，mappingReads将是对目标的相应子集读对。


值----------Value----------

If mappingReads equals FALSE, just the fraction of reads / read pairs mapping to targets is returned. When reads contains all single reads (i.e. is output of get.reads), this is the number of target-overlapping reads, divided by the number of all single reads. When reads contains read pairs (i.e. is output of reads2pairs), it is the number of read pairs with at least one target-overlapping read, divided by the number of read pairs (= half the number of reads). In case of small targets and large insert sizes the two reads of a pair could be located on both sides of the target without overlap, respectively. Still, the read pair will be counted as on-target, since the corresponding DNA molecule was covering the target.
如果mappingReads等于FALSE，只是分数的读/读双映射到目标返回。当reads包含所有单读（即是输出get.reads），这是目标重叠的读取次数，除以所有单数读取。当reads包含读对（即输出reads2pairs），它是至少有一个读对目标重叠读取，读取的双数（=一半数量的划分读）。在小目标和大刀片大小的情况下，两个一对可设的目标，双方没有重叠，分别读取。尽管如此，读对将被算作目标，因为相应的DNA分子被覆盖的目标。

If mappingReads equals TRUE, a list is returned with elements
如果mappingReads等于TRUE，列表返回元素


参数：onTargetFraction
fraction of reads / read pairs mapping to targets
分数的读/读双映射到目标


参数：mappingReads
RangedData table containing positions of the reads / read pairs mapping to target regions
RangedData表，其中包含读取的位置，读/对映射到目标区域


注意----------Note----------

With the output from fraction.target and fraction.reads.target the 'enrichment' of the target capture experiment can be calculated as
与fraction.target和fraction.reads.target“浓缩”的目标捕获实验可以计算的输出


作者（S）----------Author(s)----------


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



参见----------See Also----------

fraction.target, get.reads, reads2pairs, get.targets
fraction.target，get.reads，reads2pairs，get.targets


举例----------Examples----------


## get reads and targets[＃得到读取和目标]
exptPath <- system.file("extdata", package="TEQC")
readsfile <- file.path(exptPath, "ExampleSet_Reads.bed")
reads <- get.reads(readsfile, idcol=4, skip=0)
targetsfile <- file.path(exptPath, "ExampleSet_Targets.bed")
targets <- get.targets(targetsfile, skip=0)

## fraction of on-target reads[＃目标的一小部分内容]
fraction.reads.target(reads, targets)

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


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