alignmentData-class(segmentSeq)
alignmentData-class()所属R语言包：segmentSeq
Class "alignmentData"
类“alignmentData”
译者：生物统计家园网 机器人LoveR
描述----------Description----------
The alignmentData class records information about a set of alignments of high-throughput sequencing data to a genome. Details include the alignments themselves, details on the chromosomes of the genome to which the data are aligned, and
alignmentData类信息记录的一套高通量基因组测序数据的路线。详细信息，包括自己的路线，其中的数据是一致的基因组染色体上的细节，
类的对象----------Objects from the Class----------
Objects can be created by calls of the form new("alignmentData", ...), but more usually by using one of readBAM or readGeneric functions to generate the object from a set of alignment files.
可以创建对象的形式new("alignmentData", ...)的呼声，但更通常使用readBAM或readGeneric功能之一，以生成的对象从一组对齐文件。
插槽----------Slots----------
alignments: Object of class "GRanges".
alignments类"GRanges"的对象。
data: Object of class "DataFrame". For each alignment described in the alignments slot, contains the
data类"DataFrame"的对象。每对准对于alignments插槽描述，包含
libnames: Object of class "character". The
libnames类"character"的对象。 “
libsizes: Object of class "numeric". The
libsizes类"numeric"的对象。 “
replicates: Object of class "factor".
replicates类"factor"的对象。
Details
详情----------Details----------
The alignments slot is the key element of this class. This is a GRanges object that, in addition to the usual elements defining the location of aligned objects to a reference genome, also describes the values "tag", giving the sequence of the tag aligning to the location, "matches", indicating in how many places that tag matches to the genome, "chunk", an identifier for the sets of tags that align close enough together to form a potential locus, and "chunkDup", indicating whether that tag matches to multiple places within the chunk.
alignments槽是这个类的关键因素。这是一个GRanges对象元素通常的定义对齐对象参考基因组的位置，此外，还介绍了值“标签”，标签序列对齐的位置，“比赛“，表明在多少地方，标签匹配的基因，”块“，标识标签，对齐足够接近在一起，形成一个潜在的轨迹套，和”chunkDup“，说明，标签是否符合块内的多个地方。
The library sizes, defined in the libsizes slot, provide some scaling factor for the observed number of counts of a tag in different samples.
库的大小，定义在libsizes插槽，提供不同样品的标签计数的观测数一定的比例因子。
The replicates slot is a vector of factors such that the ith sample is a replicate of the jth sample if and only if @replicates[i] == @replicates[j].
replicates槽是一个因素，例如，第i个样本的第j个样本，如果是复制，只有@replicates[i] == @replicates[j]向量。
方法----------Methods----------
[ signature(x = "alignmentData"): ...
[signature(x = "alignmentData")...
dim signature(x = "alignmentData"): ...
朦胧signature(x = "alignmentData")：...
initialize signature(.Object = "alignmentData"): ...
初始化signature(.Object = "alignmentData")...
show signature(object = "alignmentData"): ...
显示signature(object = "alignmentData")：...
作者（S）----------Author(s)----------
Thomas J. Hardcastle
参见----------See Also----------
readGeneric, which will produce a 'alignmentData' object from appropriately formatted tab-delimited files. readBAM, which will produce a 'alignmentData' object from BAM files. processAD, which will convert an 'alignmentData' object into a 'segData' object for segmentation.
readGeneric适当格式化的制表符分隔的文件，这将产生一个'alignmentData'对象。 readBAM的BAM文件，这将产生一个'alignmentData'对象。 processAD，这将转换成一个segData对象分割'alignmentData'对象。
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)
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 13:59:20
