heuristicSeg(segmentSeq)
heuristicSeg()所属R语言包：segmentSeq
A (fast) heuristic method for creation of a genome segment map.
一个创造一个基因片段图（快）启发式的方法。
译者：生物统计家园网 机器人LoveR
描述----------Description----------
This method identifies by heuristic methods a set of loci from a segData object. It does this by identifying within replicate groups regions of the genome that satisfy the criteria for being a locus and have no region within them that satisfies the criteria for being a null. These criteria can be defined by the user or inferred from the data.
这种方法确定的启发式方法一套segData对象的位点。它通过满足作为一个轨迹的标准和区域内没有满足的标准是一个空的基因组区域内复制组确定。这些标准可以由用户定义，或从数据推断。
用法----------Usage----------
heuristicSeg(sD, aD, bimodality = TRUE, RKPM = 300, gap = 100, subRegion
= NULL, getLikes = TRUE, verbose = TRUE, cl)
参数----------Arguments----------
参数：aD
An alignmentData object.
alignmentData对象。
参数：sD
A segData object derived from the "aD" object.
一个segData广告的对象派生的对象。
参数：bimodality
Should the criteria for loci be inferred from the (likely) bimodal structure of the data?
位点的标准应被推断的双峰结构的数据（可能）？
参数：RKPM
What RKPM (reads per kilobase per million reads) distinguishes between a locus and a null region? Ignored if bimodality = TRUE.
RKPM（读取每百万碱基读取）之间的轨迹和空区域区别？如果bimodality = TRUE忽略。
参数：gap
What is the minimum length of a null region? Ignored if bimodality = TRUE.
什么是空区域的最小长度是多少？如果bimodality = TRUE忽略。
参数：subRegion
A 'data.frame' object defining the subregions of the genome to be segmented. If NULL (default), the whole genome is segmented.
一个'data.frame'对象确定的基因组，分区域分割。如果为NULL（默认），全基因组是分段的。
参数：getLikes
Should posterior likelihoods for the new segmented genome (loci and nulls) be assessed?
应该为新的分段基因组（基因位点和空）后的似然性进行评估？
参数：verbose
Should the function be verbose? Defaults to TRUE.
如果函数是冗长的吗？默认为true。
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----------
A 'cluster' object (package: snow) may be used for parallelisation of parts of this function when examining 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），可用于并行化部分的功能，研究大型数据集时。这个变量传递NULL会导致在非并行模式运行的功能。
值----------Value----------
A lociData object, containing count information on all the segments discovered.
一个lociData对象，包含在所有的细分计数信息发现。
作者（S）----------Author(s)----------
Thomas J. Hardcastle
参考文献----------References----------
RNA loci from high-throughput sequencing data. In press.
参见----------See Also----------
classifySeg, an alternative approach to this problem using an empirical Bayes approach to classify segments. plotGenome, a function for plotting the alignment of tags to the genome (together with the segments defined by this function). baySeq, a package for discovering differential expression in lociData objects.
classifySeg，这个问题，使用经验Bayes方法分类细分的一种替代方法。 plotGenome，绘制对齐标记基因（连同这个函数定义段）的功能。 baySeq，lociData对象中发现差异表达的包。
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segData“对象。]
sD <- processAD(alignData, cl = NULL)
# Use the segData object to produce a segmentation of the genome.[使用segData对象产生的基因组的分割。]
segD <- heuristicSeg(sD = sD, aD = alignData, subRegion = data.frame(chr = ">Chr1", start =
1, end = 1e5), 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。
|
发表于 2012-2-26 14:00:04
