getReadCountsFromBAM(cn.mops)
getReadCountsFromBAM()所属R语言包：cn.mops
Generates the read counts from BAM Files. These counts are necessary for CNV detection methods based on depth of coverage information. Note that the function is much faster, if the BAM files have an index file. The index file is assumed to be in the same folder and have an identical
生成的BAM文件读取计数。这些罪名是基于深度报道信息的CNV检测方法是必要的。请注意该函数的速度要快得多，BAM的文件，如果有一个索引文件。索引文件被认为是在同一文件夹具有相同的
译者：生物统计家园网 机器人LoveR
描述----------Description----------
Generates the read counts from BAM Files. These counts are necessary for CNV detection methods based on depth of coverage information. Note that the function is much faster, if the BAM files have an index file. The index file is assumed to be in the same folder and have an identical file name except that ".bai" is appended.
生成的BAM文件读取计数。这些罪名是基于深度报道信息的CNV检测方法是必要的。请注意该函数的速度要快得多，BAM的文件，如果有一个索引文件。索引文件被认为是在同一文件夹，并有一个相同的文件名，除“瞿秋白”追加。
用法----------Usage----------
getReadCountsFromBAM(BAMFiles, sampleNames, refSeqName,
WL, mode = "unpaired")
参数----------Arguments----------
参数：BAMFiles
BAMFiles
BAMFiles
参数：sampleNames
The corresponding sample names to the BAM Files.
相应的样本的BAM文件的名称。
参数：refSeqName
Name of the reference sequence that should be analyzed. The name must appear in the header of the BAM file. If it is not given the function will select the first reference sequence that appears in the header of the BAM files.
应分析参考序列的名称。该名称必须出现在头的BAM文件。如果没有给出该函数将选择第一参考序列出现在BAM的文件头。
参数：WL
Windowlength. Length of the initial segmentation of the genome in basepairs. Should be chosen such that on the average 100 reads are contained in each segment. If not given, cn.mops will try to find an appropiate window length.
windowlength。长度的基因组中碱基对的初始分割。应选择这样载在每段平均100读取。如果没有给出中，cn.mops会尝试找到一个适当的窗口长度。
参数：mode
Possible values are "paired" and "unpaired", whether the mapping algorithm was using a "paired" or "unpaired" strategy. Default = "unpaired".
可能的值是“配对”和“未成”，映射算法是否使用“配对”或“未成”战略。默认=“未成”。
值----------Value----------
An instance of "GRanges", that contains the breakpoints of the initial segments and the raw read counts that were extracted from the BAM files. This object can be used as input for cn.mops and other CNV detection methods.
“农庄”，它包含的初始段和原始读取计数，从BAM的文件中提取的断点的实例。这个对象可以被用来作为输入cn.mops和其他CNV的检测方法。
作者（S）----------Author(s)----------
Guenter Klambauer <a href="mailto:klambauer@bioinf.jku.at">klambauer@bioinf.jku.at</a>
举例----------Examples----------
BAMFiles <- list.files(system.file("extdata", package="cn.mops"),pattern=".bam$",
full.names=TRUE)
bamDataRanges <- getReadCountsFromBAM(BAMFiles,
sampleNames=paste("Sample",1:3),WL=5000)
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 15:33:33
