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

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

                                        Bait coverage versus GC content plot
                                         诱饵覆盖与GC含量的图

                                         译者：生物统计家园网 机器人LoveR

描述----------Description----------

Calculates and plots average normalized coverage per hybridization probe versus GC content
与GC含量的计算和图，平均每杂交探针归覆盖


用法----------Usage----------


coverage.GC(coverageAll, baits, returnBaitValues = FALSE, linecol = "darkred", lwd, xlab, ylab, pch, col, cex, ...)



参数----------Arguments----------

参数：coverageAll
RleList containing Rle vectors of per-base coverages for each chromosome, i.e. coverageAll output of coverage.target
RleList含Rle每个碱基覆盖每条染色体的向量，即coverageAll的coverage.target输出


参数：baits
A RangedData table holding the hybridization probe ("bait") positions and sequences, i.e. output ofget.baits
一个RangedData表（“诱饵”）持有的杂交探针位置和序列，get.baits的，即输出


参数：returnBaitValues
if TRUE, average coverage, average normalized coverage and GC content per bait are returned
如果TRUE，平均覆盖率，平均标准化覆盖率和GC含量每诱饵返回


参数：linecol, lwd
color and width of spline curve
样条曲线的颜色和宽度


参数：xlab, ylab
x- and y-axis labels
x和y轴的标签


参数：pch
plotting character
绘制字符


参数：col, cex
color and size of plotting character
绘制字符的颜色和大小


参数：...
further graphical parameters passed to plot
进一步的图形参数传递plot


Details

详情----------Details----------

The function calculates average normalized coverages for each bait: the average coverage over all bases within a bait is divided by the average coverage over all bait-covered bases. Normalized coverages are not dependent on the absolute quantity of reads and are hence better comparable between different samples
函数计算平均每个诱饵归覆盖，平均覆盖率超过所有诱饵覆盖碱基分为平均覆盖率超过所有碱基内的诱饵。规范化的覆盖范围是不依赖于读取的绝对数量和不同样品之间因此更好的可比性


值----------Value----------

A scatterplot with normalized per-bait coverages on the y-axis and GC content of respective baits on the x-axis. A smoothing spline is added to the plot.
与y轴和x轴各自的毒饵的GC含量每诱饵归覆盖的散点图。平滑样条被添加到图。

If returnBaitValues = TRUE average coverage, average normalized coverage and GC content per bait are returned
如果返回returnBaitValues = TRUE平均覆盖率，平均规范化的覆盖面和GC含量每诱饵


作者（S）----------Author(s)----------


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



参考文献----------References----------

Enrichment of sequencing targets from the human genome by solution hybridization.

参见----------See Also----------

coverage.target, covered.k, coverage.hist, coverage.plot,
coverage.target，covered.k，coverage.hist，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)

## calculate per-base coverages[＃计算每个碱基覆盖]
Coverage <- coverage.target(reads, targets, perBase=TRUE)

## get bait positions and sequences[＃诱饵的位置和序列]
baitsfile <- file.path(exptPath, "ExampleSet_Baits.txt")
baits <- get.baits(baitsfile, chrcol=3, startcol=4, endcol=5, seqcol=2)

## do coverage vs GC plot[＃做覆盖率比GC图。]
coverage.GC(Coverage$coverageAll, baits)

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


注：
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