runSigPathway(sigPathway)
runSigPathway()所属R语言包：sigPathway
Perform pathway analysis
执行途径分析
译者：生物统计家园网 机器人LoveR
描述----------Description----------
Performs pathway analysis
执行途径分析
用法----------Usage----------
runSigPathway(G, minNPS = 20, maxNPS = 500,
tab, phenotype, nsim = 1000,
weightType = c("constant", "variable"), ngroups = 2,
npath = 25, verbose = FALSE, allpathways = FALSE,
annotpkg = NULL, alwaysUseRandomPerm = FALSE)
参数----------Arguments----------
参数：G
a list containing the source, title, and probe sets associated with each curated pathway
列表包含源代码，标题和探针集相关联的每个策划途径
参数：minNPS
an integer specifying the minimum number of probe sets in tab that should be in a gene set
一个整数，指定最低数量的探针设置在tab应该是在基因组
参数：maxNPS
an integer specifying the maximum number of probe sets in tab that should be in a gene set
一个整数，指定的最大数量的探针设置在tab应该是在基因组
参数：tab
a numeric matrix of expression values, with the rows and columns representing probe sets and sample arrays, respectively
数字矩阵表达式的值，代表探针台和样品阵列的行和列，分别为
参数：phenotype
a numeric (or character if ngroups >= 2) vector indicating the phenotype
一个数字（或字符，如果ngroups> = 2）向量表示的表型
参数：nsim
an integer indicating the number of permutations to use
一个整数，指示的使用数量排列
参数：weightType
a character string specifying the type of weight to use when calculating NEk statistics
一个字符串，指定类型的重量计算NEK统计时使用
参数：ngroups
an integer indicating the number of groups in the matrix
一个整数，指示组在矩阵
参数：npath
an integer indicating the number of top gene sets to consider from each statistic when ranking the top pathways
顶级基因数目的整数，指示将考虑每个统计居顶端途径时
参数：verbose
a boolean to indicate whether to print debugging messages to the R console
一个布尔值，指示是否打印调试消息的R控制台
参数：allpathways
a boolean to indicate whether to include the top npath pathways from each statistic or just consider the top npath pathways (sorted by the sum of ranks of both statistics) when generating the summary table
一个布尔值，指示是否包括每个统计的的顶部npath途径，或只考虑顶端npath途径（由两个统计队伍的总和排序）时生成的汇总表
参数：annotpkg
a character vector specifying the name of the BioConductor annotation package to use to fetch accession numbers, Entrez Gene IDs, gene name, and gene symbols
指定的BioConductor注释包的名称，使用获取加入号码，Entrez基因标识，基因名称，基因符号字符向量
参数：alwaysUseRandomPerm
a boolean to indicate whether the algorithm can use complete permutations for cases where nsim is greater than the total number of unique permutations possible with the phenotype vector
一个布尔值，表明该算法是否可以使用完整的情况排列nsim是phenotype向量大于独特的排列总数可能
Details
详情----------Details----------
runSigPathway is a wrapper function that
runSigPathway是一个包装函数
(1) Selects the gene sets to analyze using selectGeneSets
（1）选择的基因组分析使用selectGeneSets
(2) Calculates NTk and NEk statistics using calculate.NTk and calculate.NEK
（2）计算NTK和NEK统计使用calculate.NTk和calculate.NEK
(3) Ranks the top npath pathways from each statistic using rankPathways
（3）的行列顶端npath从每个统计途径使用rankPathways
(4) Summarizes the means, standard deviation, and individual statistics of each probe set in each of the above pathways using getPathwayStatistics
（4）总结的方式，标准差，每个探针的个人统计，上述途径，每年使用getPathwayStatistics
值----------Value----------
A list containing
一份列表，列出
参数：gsList
a list containing three vectors from the output of the selectGeneSets function
一个列表，其中包含三个向量从selectGeneSets函数的输出，
参数：list.NTk
a list from the output of calculate.NTk
从输出calculate.NTk名单
参数：list.NEk
a list from the output of calculate.NEk
从输出calculate.NEk名单
参数：df.pathways
a data frame from rankPathways which contains the top pathways' indices in G, gene set category, pathway title, set size, NTk statistics, NEk statistics, the corresponding q-values, and the ranks.
从rankPathways其中的数据框包含的“顶级途径指数G，基因组类别，通路称号，集大小，NTK统计，NEK统计，相应的Q值，队伍。
参数：list.gPS
a list from getPathwayStatistics containing nrow(df.pathways) data frames corresponding to the pathways listed in df.pathways. Each data frame contains the name, mean, standard deviation, the test statistic (e.g., t-test), and the corresponding unadjusted p-value. If ngroups = 1, the Pearson correlation coefficient is also returned. If a valid annotpkg is specified, the probes' accession numbers, Entrez Gene IDs, gene name, and gene symbols are also returned.
从getPathwayStatistics包含列表nrow(df.pathways)数据框对应df.pathways上市的途径。每个数据框包含的名称，意思是，标准差，检验统计量（例如，T-测试），以及相应的未经调整的p值。如果ngroups= 1，Pearson相关系数也返回。如果一个有效的annotpkg指定的探针加入号码，Entrez基因标识，基因名称，基因符号也回来了。
参数：parameters
a list of parameters (e.g., nsim) used in the analysis
一个参数列表（例如，nsim）在分析中使用
作者（S）----------Author(s)----------
Lu Tian, Peter Park, and Weil Lai
参考文献----------References----------
P.J. (2005) Discovering statistically significant pathways in expression profiling studies. Proceedings of the National Academy of Sciences of the USA, 102, 13544-9.
举例----------Examples----------
## Load in filtered, expression data[＃加载在过滤数据，表达]
data(MuscleExample)
## Prepare the pathways to analyze and run analysis with 1 wrapper function[＃准备1包装功能的途径来分析和运行分析]
nsim <- 1000
ngroups <- 2
verbose <- TRUE
weightType <- "constant"
npath <- 25
allpathways <- FALSE
annotpkg <- "hgu133a.db"
res.muscle <- runSigPathway(G, 20, 500, tab, phenotype, nsim,
weightType, ngroups, npath, verbose,
allpathways, annotpkg)
## Summarize results[＃汇总结果]
print(res.muscle$df.pathways)
## Get more information about the probe sets' means and other statistics[＃获取更多探针集的手段和其他统计信息]
## for the top pathway in res.pathways[＃顶部在res.pathways的途径]
print(res.muscle$list.gPS[[1]])
## Write table of top-ranked pathways and their associated probe sets to[＃写表和世界排名第一的途径及其相关的探针设置]
## HTML files[＃HTML文件]
writeSigPathway(res.muscle, tempdir(), "sigPathway_rSP",
"TopPathwaysTable.html")
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。
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发表于 2012-2-26 14:17:55
