getCounts(segmentSeq)
getCounts()所属R语言包：segmentSeq
Gets counts from alignment data from a set of genome segments.
从一组基因组片段的对齐数据获取计数。
译者：生物统计家园网 机器人LoveR
描述----------Description----------
A function for extracting count data from an
用于计数数据提取功能
用法----------Usage----------
getCounts(segments, aD, preFiltered = FALSE, as.matrix = FALSE, cl)
参数----------Arguments----------
参数：segments
A GRanges object which defines a set of segments for which counts are required.
一个GRanges对象，它定义了一套计数的段。
参数：aD
An alignmentData object.
alignmentData对象。
参数：preFiltered
The function internally cleans the data; however, this may not be needed and omitting these steps may save computational time. See Details.
内部的功能清除数据;然而，这可能并不需要省略这些步骤可以节省计算时间。查看详细信息。
参数：as.matrix
If TRUE, returns the counts as a matrix. Otherwise, returns the counts as a DataFrame.
如果是TRUE，则返回一个矩阵的计数。否则，返回计数作为一个DataFrame。
参数：cl
A SNOW cluster object, or NULL. See Details.
雪聚类对象，或NULL。查看详细信息。
Details
详情----------Details----------
The function extracts count data from alignmentData object 'aD' given a set of segments. The non-trivial aspect of this function is that at a segment which contains a tag that matches to multiple places in that segment (and thus appears multiple times in the alignmentData object) should count it only once.
函数提取物计数alignmentData对象广告给定一组段的数据。这个函数的非平凡的方面是，在其中包含一个标签符合该段在多个地方（从而多次出现在alignmentData对象），它只有一次，应该算一个段。
If preFiltered = FALSE then the function allows for missing (NA) data in the segments, unordered segments and duplicated segments. If the segment list has no missing data, is already ordered, and contains no duplications, then computational time can be saved by setting preFiltered = TRUE.
如果preFiltered = FALSE那么该函数为失踪分部（NA）的数据允许，无序的重复段和段。如果段的名单有没有丢失的数据，已经是有序的，并且不包含任何重复，然后计算时间，可以保存设置preFiltered = TRUE。
A cluster object (package: snow) is recommended for parallelisation of this function when using large data sets. Passing NULL to this variable will cause the function to run in non-parallel mode.
一个cluster对象（包雪）建议使用大型数据集时，此功能的并行化。这个变量传递NULL会导致在非并行模式运行的功能。
In general, this function will probably not be accessed by the user as the processAD function includes a call to getCounts as part of the standard processing of an alignmentData object into a segData object.
在一般情况下，此功能将可能无法访问processAD函数包含作为getCounts对象的标准处理的一部分，将调用一个alignmentDatasegData用户对象。
值----------Value----------
If "as.matrix", a matrix, each column of which corresponds to a library in the alignmentData object "aD" and each row to the segment defined by the corresponding row in "segments". Otherwise an equivalent DataFrame object.
如果as.matrix“，一个矩阵，每一列对应库alignmentData对象的广告，每行由相应的行中的”分部“定义段。否则，相当于DataFrame对象。
作者（S）----------Author(s)----------
Thomas J. Hardcastle
参见----------See Also----------
processAD
processAD
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)
# Get count data for three arbitrarily chosen segments on chromosome 1.[获取数任意选择三段1号染色体上的数据。]
getCounts(segments = GRanges(seqnames = c(">Chr1"),
IRanges(start = c(1,100,2000), end = c(40,3000,5000))),
aD = 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。
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。
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发表于 2012-2-26 13:59:46
