coverage.correlation(TEQC)
coverage.correlation()所属R语言包：TEQC
Coverage correlation plot
覆盖相关图
译者：生物统计家园网 机器人LoveR
描述----------Description----------
Visualization of target coverage correlations between pairs of samples.
可视化的目标覆盖对样品之间的相关性。
用法----------Usage----------
参数----------Arguments----------
参数：coveragelist
List where each element is the output of function coverage.target, where option perBase had to be set to TRUE.
列表，其中每个元素是函数的输出coverage.target，其中选项“perBase设置TRUE。
参数：normalized
if TRUE, correlation of normalized target coverages will be shown; original coverages otherwise
如果TRUE，将会显示相关的规范化目标覆盖，否则原来的覆盖范围
参数：plotfrac
numeric value between 0 and 1. Coverages for a fraction of plotfrac of all target bases are shown.
0和1之间的数值。夜光了plotfrac的一小部分所有目标碱基。
参数：seed
seed for random selection of plotfrac bases
plotfrac碱基随机选择的种子
参数：labels
sample names that are written in the diagonal panels; if missing, names of coveragelist are taken; if those are NULL, "sample 'i'" is shown
样品名称写在对角线板;如果缺少的名字coveragelist;如果这些NULL，“样本”我“”显示
参数：main
main title
主标题
参数：pch
plot symbol for the scatter plots
积符号的散点图
参数：cex.labels, cex.pch, cex.main
sizes of sample labels, plot symbols, main title
样品标签的大小，图的符号，主标题
参数：cex.corr
size of the correlation values; if missing, sizes are made proportionally to the values of (positive) correlation.
相关值的大小，如果缺少，大小的比例（正）相关的值。
参数：font.labels, font.main
fonts for sample labels and main title
样品的标签和主标题字体
参数：...
further graphical parameters, e.g. limits and symbol color for the scatter plots
进一步的图形参数，例如限制和符号颜色的散点图
Details
详情----------Details----------
If normalized = TRUE, 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
如果normalized = TRUE，函数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----------
'pairs'-style plot where upper panels show scatter plot of (a randomly chosen fraction of) coverage values for pairs of samples. The lower panels show the respective Pearson correlation coefficients, calculated using all coverage values (even if not all of them are shown in the
的“pairs风图上面板显示分散，覆盖面值（随机选择一个分数）对样品的图。较低的面板显示采用全覆盖值（即使不是所有的人都在各自的Pearson相关系数，计算
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, covered.k, coverage.hist,
coverage.target，covered.k，coverage.hist
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)
## simulate another sample[＃模拟另一个样本]
r <- sample(nrow(reads), 0.1 * nrow(reads))
reads2 <- reads[-r,,drop=TRUE]
Coverage2 <- coverage.target(reads2, targets, perBase=TRUE)
## coverage uniformity plot[＃覆盖均匀图]
covlist <- list(Coverage, Coverage2)
coverage.correlation(covlist, plotfrac=0.1)
转载请注明:出自 生物统计家园网(http://www.biostatistic.net)。
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。
注2：由于是机器人自动翻译，难免有不准确之处，使用时仔细对照中、英文内容进行反复理解，可以帮助R语言的学习。
注3：如遇到不准确之处，请在本贴的后面进行回帖，我们会逐渐进行修订。
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发表于 2012-2-26 15:28:26
