MEDIPS.coverageAnalysis(MEDIPS)
MEDIPS.coverageAnalysis()所属R语言包：MEDIPS
The function identifies the number of CpGs (or any other predefined sequence pattern) covered by the given short reads.
功能标识的CPGs覆盖给定的短读（或任何其他预定义的序列模式）。
译者：生物统计家园网 机器人LoveR
描述----------Description----------
The main idea of the coverage analysis is to test the number of CpGs (or any other predefined sequence pattern) covered by the given short reads and to have a look at the depth of coverage. Before you can start the coverage analysis, it is necessary that you have created a MEDIPS SET and excecuted the MEDIPS.getPositions function. For the coverage analysis, the total set of available regions is divided into random subsets of equal size where the number of subsets is determined by the parameter no_iterations. The coverage analysis iteratively selects an increasing number of subsets and and tests how many CpGs are covered by the available regions. Moreover, it is tested how many CpGs are covered at least 1x, 2x, 3x, 4x, 5x, and 10x. These levels of coverage depths can be adjusted by setting the coverages parameter (see below). As the regions are typically of short length (e.g. 36bp), it is recommended to extend the region length by an extend value.
覆盖率分析的主要思路是给予短所涵盖的CPGs（或任何其他预定义的序列模式）测试的读取次数，看看在深度报道。之前就可以开始覆盖分析，这是必要的，您已经创建了一个MEDIPS SET和excecuted的MEDIPS.getPositions功能的。覆盖分析，可用区域的总分为大小相等的随机亚群的数量由参数no_iterations确定的子集。覆盖分析，反复选择，越来越多的一个子集和可用的区域覆盖多少的CPGs测试。此外，它测试的是多少的CPGs覆盖了至少1倍，2倍，3倍，4倍，5倍和10倍。这些层次覆盖深度可以调整设置覆盖参数（见下文）。由于区域通常是短长度（如36bp），它是建议延长扩展的价值区域的长度。
用法----------Usage----------
MEDIPS.coverageAnalysis(data = NULL, coverages = c(1, 2, 3, 4, 5, 10), no_iterations = 10, no_random_iterations = 1, extend = NULL)
参数----------Arguments----------
参数：data
has to be a MEDIPS SET object
是MEDIPS集对象
参数：coverages
default is c(1, 2, 3, 4, 5, 10). The coverages define the depth levels for testing how often a CpG was covered by the given regions. Just specify any other vector of coverage depths you would like to test.
默认是c（1，2，3，4，5，10）。覆盖定义为测试一个CpG如何往往是由给定的区域覆盖的深度级别。只要指定任何你想测试的覆盖深度向量。
参数：no_iterations
defines the number of subsets created from the full set of available regions (default=10).
定义从可用区域的全套（默认值= 10）创建的子集的数量。
参数：no_random_iterations
approaches that randomly select data entries may be processed several times in order to obtain more stable results. By specifying the no_random_iterations parameter (default=1) it is possible to run the coverage analysis several times. The final results returned to the coverage results object are the averaged results of each random iteration step.
可处理的方法，随机选取数据项几次，以获得更稳定的结果。通过指定no_random_iterations参数（默认值= 1），它是可以多次运行覆盖分析。返回到覆盖效果对象的最终结果是每个随机迭代步的平均结果。
参数：extend
extends the region lengths before the coverage analysis is performed.
前进行覆盖分析，该区域的长度延伸。
值----------Value----------
参数：matrix
Contains the number of covered CpGs in each iteration (rows) and for different levels of coverages (columns)
包含在每个迭代（行）和不同层次的覆盖（列）的数量，覆盖的CPGs
参数：maxPos
is the total number of sequence patterns (e.g. CpGs) within the refernce genome
是总数（例如的CPGs）内refernce基因组序列模式
参数：pattern
is the defined sequence pattern
定义的序列模式
参数：coveredPos
shows the number of covered sequence pattern (e.g. CpGs) using the total set of available regions for several depths of coverages (columns). The last row shows the percentage of covered sequence pattern relative to the total number of available sequence patterns within the reference genome.
显示覆盖的序列模式使用几个深度覆盖（列）可用区域的总集（例如的CPGs）的数量。最后一行显示内的参考基因组序列模式总数的比例相对覆盖的序列模式。
作者（S）----------Author(s)----------
Lukas Chavez
举例----------Examples----------
library(BSgenome.Hsapiens.UCSC.hg19)
file=system.file("extdata", "MeDIP_hESCs_chr22.txt", package="MEDIPS")
CONTROL.SET = MEDIPS.readAlignedSequences(BSgenome="BSgenome.Hsapiens.UCSC.hg19", file=file)
CONTROL.SET = MEDIPS.getPositions(data = CONTROL.SET, pattern = "CG")
cr.control = MEDIPS.coverageAnalysis(data = CONTROL.SET, extend = 400, no_iterations = 10)
cr.control
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 00:37:33
