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

loveR

duplicates.barplot(TEQC)
duplicates.barplot()所属R语言包：TEQC

                                        Read duplicates barplot
                                         阅读重复barplot

                                         译者：生物统计家园网 机器人LoveR

描述----------Description----------

Barplot showing fractions of reads / read pairs which are unique and for which there are two, three, ... copies.
barplot显示分数的读，读/对是独一无二的，其中有两个，三个......副本。


用法----------Usage----------


duplicates.barplot(reads, targets, returnDups=FALSE, truncateX, col=c("red","lightblue"), xlab, ylab, ylim, ...)



参数----------Arguments----------

参数：reads
RangedData table containing positions of sequenced reads, i.e. output from get.reads. Alternatively, for paired-end data, it can be the output of reads2pairs when multiplicities of read pairs instead of fraction of single reads shall be visualized.
RangedData从get.reads表，其中包含的测序读，即输出的位置。另外，配对末端数据，它可以是reads2pairs当多重的，而不是单一的读取分数只读对可视化的输出。


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：returnDups
if TRUE, on- and off-target read / read pair multiplicities are returned
如果TRUE，和脱靶读/读对多重返回


参数：truncateX
integer; show bars only up to a read / read pair multiplicity of truncateX (x-axis)
整数;秀条形只有一个truncateX（X轴）读/读对多重


参数：col
vector specifying the two colors of bars and legend for on- and off-target read multiplicities
向量和脱靶指定两种颜色的条形和传奇的多重阅读


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


参数：ylim
y-axis coordinate ranges
Y轴坐标范围


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


Details

详情----------Details----------

Single-end reads are considered as duplicates if they have same start end end position. Paired-end read pairs are considered as duplicates if start and end positions of both reads of the pairs are identical. Usually, duplicates are removed before further analyses (e.g. SNP detection), because they could represent PCR artefacts. However, in target capture experiments it is likely to have also many "real" duplicates (actual different molecules that happen to start at same position) due to the "enrichment" of the target regions. The separation in the barplot between on- and off-target reads / read pairs gives an impression on whether on-target there are more reads with higher multiplicites, which hence might indicate a reasonable amount of "real" duplication. A paired-end read pair is considered on-target if at least one of its reads
单端读取被视为重复，如果他们有相同的开始月底结束的位置。如果双方的对读取的起始和结束位置是相同的配对末端读取对被视为重复。通常情况下，复制被删除前进一步分析（如SNP检测），因为他们代表的PCR文物。然而，在目标捕获实验很可能有也有许多“真正的”重复（实际不同的分子，发生在相同的位置开始），由于“致富”的目标区域。上和脱靶之间在barplot的分离读/读对目标是否有更多更高的multiplicites，因此可能表明一个“真正的”重复的合理数量的读取给人一个印象。对被认为是一个配对末端读取目标如果至少有一个它的读取


值----------Value----------

Barplot where the bar heights correspond to fractions of reads / read pairs which are present in the data with the respective number of copies (x-axis). Fractions are calculated separately for on- and off-target reads / read pairs. A read pair is considered on-target if at least one of its reads overlaps with a target. Absolute numbers (in millions) are additionally written on top of the bars.
barplot栏高度对应读取的分数，读/双，这是目前在各自的副本数量（X轴）的数据。分别计算和脱靶读/读双组分。读对被认为是目标，如果至少有读取与重叠的目标之一。此外书面绝对数量（百万美元）的条形之上。

If returnDups equals TRUE, a list with two elements absolute and relative is returned. The former is a matrix that contains the absolute numbers of reads / read pairs for each multiplicity (columns), for both on- and off-target reads / read pairs (rows).
如果returnDups等于TRUE，absolute和relative返回两个元素的列表。前者是一个矩阵，包含读取绝对数读/对每个多重（列），和脱靶读/读对（行）。


作者（S）----------Author(s)----------


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



参见----------See Also----------

get.reads, reads2pairs, get.targets
get.reads，reads2pairs，get.targets


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)

## duplicates barplot for single reads[＃单一读取重复barplot]
duplicates.barplot(reads, targets, returnDups=TRUE)

## duplicates barplot for read pairs[＃只读对重复barplot]
readpairs <- reads2pairs(reads)
duplicates.barplot(readpairs, targets, returnDups=TRUE)

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。