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

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coverage.target(TEQC)
coverage.target()所属R语言包：TEQC

                                        Calculates read coverage
                                         计算读取覆盖

                                         译者：生物统计家园网 机器人LoveR

描述----------Description----------

Calculates average coverage over all target bases, average coverage for each target separately,
计算平均覆盖率超过所有目标的基础上，平均覆盖率分别为每个目标


用法----------Usage----------


coverage.target(reads, targets, Offset = 0, perTarget = TRUE, perBase = TRUE)



参数----------Arguments----------

参数：reads
RangedData table containing positions of sequenced reads, i.e. output from get.reads
RangedDataget.reads表，其中包含的测序读，即输出的位置


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：perTarget
if TRUE, coverage average and standard deviation per target are calculated and returned
如果为TRUE，覆盖每个目标偏差的平均值和标准计算并返回


参数：perBase
if TRUE, the per-base coverages i) only for targeted bases and ii) for all sequenced and/or targeted bases, are returned
如果为TRUE，每个碱基覆盖）所有测序和/或有针对性的碱基，只为有针对性的碱基和II），返回


值----------Value----------

A list is returned with elements
返回一个列表的元素


参数：avgTargetCoverage
average coverage over all target bases
平均覆盖所有目标碱基


参数：targetCoverageSD
standard deviation of coverage of all target bases
覆盖所有目标碱基的标准偏差


参数：targetCoverageQuantiles
0% (minium), 25%, 50% (median), 75% and 100% (maximum) quantiles of coverage of all target bases
所有的目标碱基覆盖0％（minium），25％，50％（中位数），75％和100％（最高）位数


参数：targetCoverages
Input RangedData table targets with two additional 'values' columns avgCoverage and coverageSD. The former contains the average coverage for each target, the latter the respective coverage standard deviation. Only returned if perTarget equals TRUE.
输入RangedData表targets另外两个“值”列avgCoverage和coverageSD。前者包含的平均覆盖率为每一个目标，后者各自的覆盖标准偏差。仅返回perTarget等于TRUE的。


参数：coverageAll
RleList containing a Rle vector for each chromosome with coverages for all bases that are sequenced and/or within a targeted; only returned if perBase equals TRUE
RleList每一个染色体含有Rle向量覆盖所有测序和/或在有针对性的碱基;只返回perBase等于TRUE


参数：coverageTarget
RleList containing a Rle vector for each chromosome with coverages for target bases only; only returned if perBase equals TRUE
RleList每一个染色体含有Rle只为目标碱基覆盖的向量，只有返回perBase等于TRUE


作者（S）----------Author(s)----------


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



参见----------See Also----------

covered.k, coverage.hist, coverage.uniformity, coverage.plot,
covered.k，coverage.hist，coverage.uniformity，coverage.plot


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)

## total average, per-base and per-target coverages[＃总平均，每个碱基，每个目标的覆盖范围]
Coverage <- coverage.target(reads, targets)

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


注：
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