coverage.uniformity(TEQC)
coverage.uniformity()所属R语言包：TEQC
Coverage uniformity plot
覆盖均匀图
译者：生物统计家园网 机器人LoveR
描述----------Description----------
Visualization of target coverage uniformity. A line shows the cumulative fraction
可视化的目标，覆盖均匀。 A线显示累积分数
用法----------Usage----------
coverage.uniformity(coveragelist, addlines = TRUE, add = FALSE, xlab, ylab, xlim, ylim, col, lwd, ...)
参数----------Arguments----------
参数：coveragelist
output of function coverage.target, where option perBase had to be set to TRUE, i.e. a list with elements coverageTarget and avgTargetCoverage
输出功能coverage.target，其中选项“perBaseTRUE，即必须设置一个元素的列表coverageTarget和avgTargetCoverage
参数：addlines
if TRUE, dashed lines are added to the plot that indicate the fractions of bases achieving at least the average or at least half the average coverage
如果TRUE，虚线的图表明碱基的比例至少达到平均或至少有一半的平均覆盖率增加
参数：add
if TRUE, the coverage uniformity line of a new sample is added to an already existing plot
如果TRUE，一个新的样本覆盖均匀线被添加到一个已经存在的图
参数：xlab, ylab
x- and y-axis labels
x和y轴的标签
参数：xlim, ylim
x- and y-axis coordinate ranges
x和y轴坐标范围
参数：col
line color
线条颜色
参数：lwd
line width
线宽
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 normalized coverages: per-base coverages divided by average coverage over all targeted bases. Normalized coverages are not dependent on the absolute quantity of reads and are hence better comparable between different samples
函数的计算归覆盖除以平均覆盖率超过所有针对碱基每个碱基覆盖。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----------
Line plot showing the fraction of targeted bases (y-axis) achieving a normalized coverage of at least x. The x-axis by default is truncated at 1, which corresponds to the average normalized coverage. The steeper the curve is falling, the less uniform is the coverage. If addlines = TRUE, dashed lines indicate the fractions of bases achieving at
实现归覆盖率至少x线图显示的针对性碱基的一小部分（Y轴）。 1默认情况下，x轴被截断，相当于平均归覆盖。陡峭的曲线下降，不太均匀的覆盖面。如果addlines = TRUE，虚线表示实现在碱基的分数
作者（S）----------Author(s)----------
Manuela Hummel <a href="mailto:manuela.hummel@crg.es">manuela.hummel@crg.es</a>
参考文献----------References----------
Solution hybrid selection with ultra-long oligonucleotides for massively parallel targeted sequencing. Nat Biotechnol. 2009; 27(2): 182-9.
参见----------See Also----------
coverage.target, covered.k, coverage.hist, coverage.density,
coverage.target，covered.k，coverage.hist，coverage.density
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)
## coverage uniformity plot[＃覆盖均匀图]
coverage.uniformity(Coverage)
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注：
注1：为了方便大家学习，本文档为生物统计家园网机器人LoveR翻译而成，仅供个人R语言学习参考使用，生物统计家园保留版权。
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发表于 2012-2-26 15:29:19
