countBamInGRanges(exomeCopy)
countBamInGRanges()所属R语言包：exomeCopy
Count reads from BAM file in genomic ranges
伯爵在基因组范围内读取从BAM文件
译者：生物统计家园网 机器人LoveR
描述----------Description----------
Counts the number of reads with a specified minimum mapping quality from BAM files in genomic ranges specified by a GRanges object. This is a convenience function for counting the reads in ranges covering the targeted regions, such as the exons in exome enrichment experiments, from each sample. These read counts are used by exomeCopy in predicting CNVs in samples.
计数读取指定最低的BAM文件映射在基因组范围由农庄对象指定的质量。这是一个方便的功能范围覆盖目标区域，如从每个样品中的外显子组的富集实验的外显子，读取计数。这些读计数用于预测样品中的CNVsexomeCopy。
With the default setting (read.width=1), only the read starts are used for counting purposes (the leftmost position regardless of the strandedness of the read).
使用默认设置（read.width= 1），仅读开始用于计数的目的（最左边的位置，无论读strandedness）。
The function subdivideGRanges can be used first to subdivide ranges of different size into ranges of nearly equal width.
函数subdivideGRanges可以先用细分为不同大小的范围几乎相等宽度范围。
The BAM file requires a associated index file (see the man page for indexBam in the Rsamtools package).
在BAM文件需要一个相关的索引文件（见indexBam在Rsamtools包手册页）。
用法----------Usage----------
countBamInGRanges(bam.file,granges,min.mapq=1,read.width=1)
参数----------Arguments----------
参数：bam.file
The path of the BAM file for the sample to be counted.
样品的BAM文件路径计算。
参数：granges
An object of type GRanges with the ranges in which to count reads.
读取一个对象的类型与范围在数农庄。
参数：min.mapq
The minimum mapping quality to count a read. Defaults to 1. Set to 0 for counting all reads.
最低的测绘质量来算一读。默认为1。所有读取计数设置为0。
参数：read.width
The width of a read, used in counting overlaps of mapped reads with the genomic ranges. The default is 1, resulting in the counting of only read starts in genomic ranges. If the length of fixed width reads is used, e.g. 100 for 100bp reads, then the function will return the count of all overlapping reads with the genomic ranges. However, counting all overlapping reads introduces dependency between the counts in adjacent windows.
一读，在映射的计数重叠的宽度与基因组范围内读取。默认值是1，只读在基因组范围内开始计数。如果使用固定宽度的长度读取，例如： 100 100bp的读，那么该函数将返回读取与基因组范围内的所有重叠的罪名。然而，计数所有重叠的内容介绍了在相邻窗口的数量之间的依赖性。
值----------Value----------
A vector giving the number of reads over the input GRanges
一个向量，使数量读取在输入农庄
参见----------See Also----------
Rsamtools GRanges subdivideGRanges
RsamtoolsGRangessubdivideGRanges
举例----------Examples----------
## get subdivided genomic ranges covering targeted region[＃得到细分的基因组范围覆盖目标区域]
## using subdivideGRanges()[＃使用subdivideGRanges（）]
example(subdivideGRanges)
## BAM file included in Rsamtools package[＃的BAM文件中Rsamtools包包含]
bam.file <- system.file("extdata", "mapping.bam", package="exomeCopy")
## create RangedData object to store read counts[＃创建RangedData对象存储读取计数]
rdata <- RangedData(space=seqnames(target.sub),ranges=ranges(target.sub))
## extract read counts from the BAM file in these genomic ranges[＃从BAM文件中提取这些基因组范围的读取计数]
rdata[["sample"]] <- countBamInGRanges(bam.file,target.sub)
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。
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发表于 2012-2-25 17:18:11
