tabulate.pvals(SIM)
tabulate.pvals()所属R语言包：SIM
Sums significant P-values for the analyzed regions
款项显著P值的分析区域
译者：生物统计家园网 机器人LoveR
描述----------Description----------
Generates a data.frame with the significance of P-values in the analyzed regions, dividing them into bins.
生成与P值在分析区域的意义data.frame，把它们划分成箱。
用法----------Usage----------
tabulate.pvals(input.regions = "all chrs",
adjust.method = "BY",
bins = c(0.001, 0.005, 0.01, 0.025, 0.05, 0.075, 0.1, 0.2, 1),
significance.idx = 8,
order.by,
decreasing = TRUE,
method = c("full", "smooth", "window", "overlap"),
run.name = "analysis_results")
参数----------Arguments----------
参数：input.regions
vector indicating the dependent regions to be analyzed. Can be defined in four ways: 1) predefined input region: insert a predefined input region, choices are: “all chrs”, “all chrs auto”, “all arms”, “all arms auto” In the predefined regions “all arms” and “all arms auto” the arms 13p, 14p, 15p, 21p and 22p are left out, because in most studies there are no or few probes in these regions. To include them, just make your own vector of arms. 2) whole chromosome(s): insert a single chromosome or a list of chromosomes as a vector: c(1, 2, 3). 3) chromosome arms: insert a single chromosome arm or a list of chromosome arms like c("1q", "2p", "2q"). 4) subregions of a chromosome: insert a chromosome number followed by the start and end position like "chr1:1-1000000" These regions can also be combined, e.g. c("chr1:1-1000000","2q", 3). See integrated.analysis for more information.
vector表明依赖区域进行分析。可以定义在四个方面：1) predefined input region: 插入一个预定义的输入区域，选择是：“所有CHRS”，“所有CHRS汽车”，“武器”，“所有武器的汽车”在预定区域“所有武器”和“所有自动武器”的武器，13P，14P，15P，21P和22P冷落，因为在大多数研究中，有没有在这些区域或几个探针。包括他们，才使自己的武器向量。 2) whole chromosome(s): 插入一个vector:c(1, 2, 3)的一个单一的染色体或染色体列表。 3) chromosome arms: 插入一个单一的染色体或染色体臂像c("1q", "2p", "2q")名单。 4) subregions of a chromosome: 插入一个染色体数目的开始和结束位置，如"chr1:1-1000000"这些区域也可以结合，如c("chr1:1-1000000","2q", 3)。看到integrated.analysis更多信息。
参数：adjust.method
Method used to adjust the P-values for multiple testing, see p.adjust. Default is “BY” recommended when copy number is used as dependent data. See SIM for more information about adjusting P-values.
用于调整多个测试P值的方法，看到p.adjust“。默认是“加”拷贝数时，建议使用相关数据。关于调整P值的更多信息，请参阅SIM卡。
参数：bins
vector of significance thresholds. This function will calculate the number of features having a P-value lower than the bin.
vector意义阈值。此函数将计算功能，有一个P-值比垃圾桶的数量。
参数：significance.idx
Index of “bins” to use when computing the percentage of significant P-values. Defaults to 8 (i.e. the first entry in “bins”), in this case 0.20.
指数显著P值的百分比计算时使用的“垃圾箱”。 8默认值（即在“垃圾箱”的第一项），在这种情况下0.20。
参数：order.by
Column used for sorting the table. Defaults to "%" (i.e. the percentage of significant p-values).
列用于排序表。默认为“％”（即显著p值的百分比）。
参数：decreasing
Direction used for sorting. Defaults to TRUE (i.e. highest values on top).
用于排序的方向。默认为true（即最高最高值）。
参数：method
this must be the either full, window, overlap or smooth but the data should generated by the same method in integrated.analysis.
这必须是要么全，窗口，重叠或顺利，但数据应产生同样的方法在integrated.analysis。
参数：run.name
This must be the same a given to integrated.analysis
这必须是相同的一个给定的integrated.analysis
值----------Value----------
Returns a data.frame. Each row corresponds to a chromosome and has as many entries as entries in bins, plus 1. Each entry contains the number of P-values that is smaller or equal to the corresponding entry in bins.
返回data.frame。每一行对应一个染色体，并有许多条目，箱中的条目，加1。每个条目包含P值小于或等于相应的条目在垃圾箱的数量。
The last entry holds the percentage of P-values that is smaller than or equal to the bin identified by significance.idx.
最后一个条目拥有的P-值的百分比小于或等于significance.idx确定的bin。
作者（S）----------Author(s)----------
Marten Boetzer, Melle Sieswerda, Renee X. de Menezes <a href="mailto:R.X.Menezes@lumc.nl">R.X.Menezes@lumc.nl</a>
参见----------See Also----------
SIM, tabulate.top.dep.features, tabulate.top.indep.features
SIM卡，tabulate.top.dep.features，tabulate.top.indep.features
举例----------Examples----------
#first run example(assemble.data)[第一次运行的例子（assemble.data）]
#and example(integrated.analysis)[和例如（integrated.analysis）]
tabulate.pvals(input.regions="8q",
adjust.method="BY",
bins=c(0.001,0.005,0.01,0.025,0.05,0.075,0.10,0.20,1.0),
run.name="chr8q")
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 14:24:49
