segmentSeq-package(segmentSeq)
segmentSeq-package()所属R语言包：segmentSeq
Segmentation of the genome based on multiple samples of high-throughput sequencing data.
分割多个样品的高通量测序数据为基础的基因组。
译者：生物统计家园网 机器人LoveR
描述----------Description----------
The segmentSeq package is intended to take multiple samples of high-throughput data (together with replicate information) and identify regions of the genome which have a (reproducibly) high density of tags aligning to them. The package was developed for use in identifying small RNA precursors from small RNA sequencing data, but may also be useful in some mRNA-Seq and chIP-Seq applications.
segmentSeq包旨在采取多个样品的高通量数据（连同复制信息），并识别标签对准他们的高密度（重复性）的基因组区域。在确定小RNA前体小分子RNA测序数据包的开发，但也可能是有用的mRNA-Seq的和SEQ芯片应用的一些。
Details
详情----------Details----------
To use the package, we construct an alignmentData object from sets of alignment files using either the readGeneric function to read text files or the readBAM function to read from BAM format files.
使用的软件包，我们构造alignmentData对象对齐文件套使用readGeneric函数读取文本文件或readBAM函数读取的BAM格式的文件。
We then use the processAD function to identify all potential subsegments of the data and the number of tags that align to these subsegments. We then use either a heuristic or empirical Bayesian approach to segment the genome into "loci" and "null" regions. We can then acquire posterior likelihoods for each set of replicates which tell us whether a region is likely to be a locus or a null in that replicate group.
然后，我们使用processAD功能，以确定潜在的数据和标签对准这些子段的所有子段。然后，我们使用一个段启发式或经验贝叶斯方法的基因组到“位点”和“空”的区域。然后，我们可以为每个复制的一套收购后的似然性，它告诉我们一个区域是否有可能是一个基因或一空，复制组。
The segmentation is designed to be usable by the baySeq package to allow differential expression analyses to be carried out on the discovered loci.
分割的设计是可用的baySeq包允许被发现的位点进行差异表达分析。
The package (optionally) makes use of the 'snow' package for parallelisation of computationally intensive functions. This is highly recommended for large data sets.
包（可选）使用并行化计算密集型功能包的“雪花”。这是强烈建议对于大型数据集。
See the vignette for more details.
看到更多细节的小插曲。
作者（S）----------Author(s)----------
Thomas J. Hardcastle
Maintainer: Thomas J. Hardcastle <tjh48@cam.ac.uk>
参考文献----------References----------
RNA loci from high-throughput sequencing data. In press.
参见----------See Also----------
baySeq
baySeq
举例----------Examples----------
# Define the chromosome lengths for the genome of interest.[定义感兴趣的基因组染色体长度。]
chrlens <- c(2e6, 1e6)
# Define the files containing sample information.[定义文件包含样本信息。]
datadir <- system.file("extdata", package = "segmentSeq")
libfiles <- c("SL9.txt", "SL10.txt", "SL26.txt", "SL32.txt")
# Establish the library names and replicate structure.[建立图书馆的名称和复制结构。]
libnames <- c("SL9", "SL10", "SL26", "SL32")
replicates <- c(1,1,2,2)
# Process the files to produce an 'alignmentData' object.[处理文件，以生产alignmentData“对象。]
alignData <- readGeneric(file = libfiles, dir = datadir, replicates =
replicates, libnames = libnames, chrs = c(">Chr1", ">Chr2"), chrlens =
chrlens, gap = 100)
# Process the alignmentData object to produce a 'segData' object.[处理的alignmentData的对象产生一个segData对象。]
sD <- processAD(alignData, cl = NULL)
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 2012-2-26 14:01:03
