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

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

                                        Coverage histogram
                                         覆盖直方图

                                         译者：生物统计家园网 机器人LoveR

描述----------Description----------

Histogram and cumulative density of target base coverages
直方图和累积密度的目标基本覆盖


用法----------Usage----------


coverage.hist(coverageTarget, col.hist = "lightblue", col.line = "orange", covthreshold, breaks = "Sturges", xlab, ylab, main, lwd, ...)



参数----------Arguments----------

参数：coverageTarget
RleList containing Rle vectors of per-target-base coverages for each chromosome, i.e. coverageTarget output from coverage.target
RleList含Rle每个目标基本覆盖每个染色体，即coverageTarget输出的向量从coverage.target


参数：col.hist
histogram color
直方图的颜色


参数：col.line
color of the cumulative density line
累计密度线的颜色


参数：covthreshold
indicates with dashed vertical and horizontal lines, which fraction of bases has a coverage of at least covthreshold; if missing, no dashed lines are drawn
虚线垂直线和水平线表示，该碱基的一小部分有一个覆盖至少covthreshold;如果缺少，无虚线绘制


参数：breaks
number of cells for the histogram, or string naming an algorithm to compute the number of cells, or function to compute the number of cells, or vector giving the breakpoints between histogram cells (see ?hist) but the latter option only with equidistant breakpoints
直方图，或字符串命名的算法，计算单元的数量，或函数来计算单元数量，或向量之间柱状图单元给予断点（见?hist），但后者只与单元的数目等距离的断点


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


参数：main
plot title
图标题


参数：lwd
line width
线宽


参数：...
further graphical parameters, passed to plot(histogram)
进一步的图形参数，传递plot(histogram)的


值----------Value----------

Histogram of read coverages for bases within the target. Additionally, a line and the right axis indicate the cumulative fraction of target bases with coverage of at least x. If option covthreshold is specified, red dashed lines highlight the cumulative fraction
直方图读覆盖的目标内的碱基。此外，一条线，右轴表示与目标碱基的累积分数至少在X的覆盖面。如果选项“covthreshold指定，红色虚线突出的累积分数


作者（S）----------Author(s)----------


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



参见----------See Also----------

coverage.target, coverage.uniformity, coverage.density, coverage.plot,
coverage.target，coverage.uniformity，coverage.density，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)

## coverage histogram[＃覆盖直方图]
coverage.hist(Coverage$coverageTarget, covthreshold=8)

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


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