sim.data.p.values(PatientGeneSets)
sim.data.p.values()所属R语言包：PatientGeneSets
Simulates data and performs gene-set analysis methods on the simulated datasets.
模拟数据和模拟数据集上执行的基因组分析方法。
译者：生物统计家园网 机器人LoveR
描述----------Description----------
This function simulates data under the passenger or permutation null, either under the null or including spiked-in gene-sets. It then calculates the p-values and q-values for all the selected gene-set analysis methods.
此功能模拟乘客或置换空下的数据，无论是在空或包括钉在基因组。然后计算p值的所有选定的基因组分析方法和Q值。
用法----------Usage----------
sim.data.p.values(EventsBySample,
Mutations,
GeneSizes,
Coverage,
GeneSets,
passenger.rates = t(data.frame(0.55*rep(1.0e-6,25))),
ID2name,
BH = TRUE,
nr.iter,
pass.null = FALSE,
perc.samples = NULL,
spiked.set.sizes = NULL,
gene.method = TRUE,
perm.null.method = TRUE,
perm.null.het.method = TRUE,
pass.null.method = TRUE,
pass.null.het.method = TRUE,
show.iter,
KnownMountains = c("EGFR","SMAD4","KRAS",
"TP53","CDKN2A","MYC","MYCN","PTEN","RB1"),
exclude.mountains=TRUE)
参数----------Arguments----------
参数：EventsBySample
Data frame giving the specific mutations for each gene and each tumor sample. See EventsBySampleBrain for an example.
数据框给每个基因和每个肿瘤样本中特定的基因突变。看到EventsBySampleBrain的一个例子。
参数：Mutations
Data frame with mutation information broken down by gene, phase and mutation type. See MutationsBrain for an example.
数据框的基因，相位和突变类型划分的突变信息。看到MutationsBrain的一个例子。
参数：GeneSizes
Data frame of gene sizes. See GeneSizes08 object for an example.
基因大小的数据框。看到GeneSizes08一个例子的对象。
参数：Coverage
Data frame with coverage information, by gene, phase, and type. See WoodCoverageBrain for an example.
数据框覆盖信息，基因，相位和类型。看到WoodCoverageBrain的一个例子。
参数：GeneSets
An object which annotates genes to gene-sets; it can either be a list with each component representing a set, or an object of the class AnnDbBimap.
一个对象，诠释基因组的基因，它可以是每个组件代表一组，或的类AnnDbBimap的对象名单。
参数：passenger.rates
Data frame with 1 row and 25 columns, of passenger mutation rates per nucleotide, by type, or "context". Columns denote types and must be in the same order as the first 25 columns in the MutationsBrain objects.
数据框1行25列，乘客每核苷酸突变率，类型，或“背景”。列表示类型，必须是在相同的顺序为第25列MutationsBrain对象。
参数：ID2name
Vector mapping the gene identifiers used in the GeneSets object to the gene names used in the other objects; if they are the same, this parameter is not needed. See ID2name for an example.
矢量测绘基因的GeneSets使用的标识符，反对基因在其他对象中使用的名称;如果它们是相同的，不需要此参数。看到ID2name的一个例子。
参数：BH
If set to TRUE, uses the Benjamini-Hochberg method to get q-values; if set to FALSE, uses the Storey method from the qvalue package.
如果设置为TRUE，使用Benjamini Hochberg方法来得到Q值，如果设置为FALSE使用qvalue包层的方法。
参数：nr.iter
The number of iterations to be simulated.
要模拟的迭代次数。
参数：pass.null
If set to true TRUE, implements the passenger null hypothesis, using the rates from passenger.rates; otherwise, implements the permutation null, permuting mutational events.
如果设置为trueTRUE，实现客运的零假设，使用的利率从passenger.rates;否则，实现置换空，置换突变事件。
参数：perc.samples
Vector representing the probabilities of the spiked-in gene-sets being altered in any given sample, as percentages; for example perc.samples = c(75, 90) means that these probabilities are 0.75 and 0.90.
概率向量代表的尖刺，在基因组正在改变在任何给定的样本，以百分比，例如perc.samples = c(75, 90)意味着这些概率是0.75和0.90。
参数：spiked.set.sizes
Vector representing the sizes, in genes, of the spiked-in gene-sets; for example, if perc.samples = c(75, 90) and spiked.set.sizes = c(50, 100), there would be 4 spiked-in sets, one with 50 genes and probability of being altered of 0.75 in each sample, one with 50 genes and probability of being altered of 0.90 in each sample, one with 100 genes and probability of being altered of 0.75 in each sample, and one with 100 genes and probability of being altered of 0.90 in each sample.
向量代表在基因的大小，钉在基因组;例如，如果perc.samples = c(75, 90)和spiked.set.sizes = c(50, 100)，将有4钉在台套，有50个基因和存在的可能性之一0.75改变每个样本中，50个基因和0.90改变在每个样品的概率，一个有100个基因和0.75改变在每个样品的概率，并与100个基因和0.90改变的可能性之一每个样品。
参数：gene.method
If set to TRUE, implements gene-oriented method.
如果设置为TRUE，实行基因导向的方法。
参数：perm.null.method
If set to TRUE, implements patient-oriented method with permutation null and no heterogeneity.
如果设置为TRUE置换空和无异质性，实现以病人为导向的方法。
参数：perm.null.het.method
If set to TRUE, implements patient-oriented method with permutation null and heterogeneity.
如果设置为TRUE置换空和异质性，实现以病人为导向的方法。
参数：pass.null.method
If set to TRUE, implements patient-oriented method with passenger null and no heterogeneity.
如果设置为TRUE乘客空和无异质性，实现以病人为本的方法。
参数：pass.null.het.method
If set to TRUE, implements patient-oriented method with passenger null and heterogeneity.
如果设置为TRUE，实现以病人为导向的方法，与乘客的空性和异质性。
参数：show.iter
If set to TRUE, shows what simulation is currently running.
如果设置为TRUE，什么模拟正在运行。
参数：KnownMountains
Vector of genes to be excluded from the permutation null simulations if exclude.mountains = TRUE.
被排除如果exclude.mountains = TRUE置换空模拟的基因向量。
参数：exclude.mountains
If set to TRUE, excludes the genes in KnownMountains.
如果设置为TRUE，排除KnownMountains.的基因
值----------Value----------
An object of the class SetMethodsSims. See SetMethodsSims for more details.
类SetMethodsSims对象。看到SetMethodsSims更多细节。
作者（S）----------Author(s)----------
Simina M. Boca, Giovanni Parmigiani.
参考文献----------References----------
Parmigiani G. Patient-oriented gene-set analysis for cancer mutation data. Submitted, 2010.
Velculescu VE, Vogelstein B. Statistical methods for the analysis of cancer genome sequencing data. http://www.bepress.com/jhubiostat/paper126/
Controlling the false discovery rate: a practical and powerful approach to multiple testing. Journal of the Royal Statistical Society B, 57:289-300, 995.
Statistical significance for genome-wide experimens. Proceedings of the National Academy of Sciences. doi: 10.1073/pnas.1530509100
Carter H, Siu I, et al. An Integrated Genomic Analysis of Human Glioblastoma Multiforme. Science. DOI: 10.1126/science.1164382
Boca SM, Barber T, Ptak J, et al. The Genomic Landscapes of Human Breast and Colorectal Cancer. Science. DOI: 10.1126/science.1145720
参见----------See Also----------
SetMethodsSims-class, CoverageBrain, EventsBySampleBrain, GeneSizes08, MutationsBrain, ID2name extract.sims.method, combine.sims
SetMethodsSims-class，CoverageBrain，EventsBySampleBrain，GeneSizes08，MutationsBrain，ID2nameextract.sims.method，combine.sims
举例----------Examples----------
##Note that this takes a few minutes to run:[＃注意，这需要几分钟的时间来运行：]
library(KEGG.db)
data(Parsons)
data(ID2name)
set.seed(831984)
resultsSim <-
sim.data.p.values(EventsBySample = EventsBySampleBrain,
Mutations = MutationsBrain,
GeneSizes = GeneSizes08,
Coverage = CoverageBrain,
GeneSets = KEGGPATHID2EXTID[c("hsa05213",
"hsa05223", "hsa00250")],
ID2name = ID2name,
nr.iter = 2,
pass.null = TRUE,
perc.samples = c(75, 95),
spiked.set.sizes = c(50),
show.iter = TRUE,
gene.method = FALSE,
perm.null.method = TRUE,
perm.null.het.method = FALSE,
pass.null.method = TRUE,
pass.null.het.method = FALSE)
resultsSim
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 10:24:46
