# #——回声= FALSE - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - knitr:: opts_chunk设置美元(崩溃= FALSE,评论= " # > ",fig.pos = ' H ') # # - - - - - eval = TRUE,消息= FALSE,警告= FALSE,结果=“隐藏”- - - - - - - - - - - - -如果(# !requireNamespace (“BiocManager”,悄悄地= TRUE)) # install.packages (BiocManager) # BiocManager::安装(“PathwaySplice”)库(PathwaySplice) # # - - - - - eval = FALSE - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - #库(devtools) # install_github (“SCCC-BBC / PathwaySplice”) # # - - - - - eval = TRUE,警告= FALSE,消息= FALSE,结果=“标记”- - - - - - - - - - - -数据(featureBasedData)头(featureBasedData) # # - - - - - eval = TRUE,消息= FALSE,警告= FALSE,结果=“标记”- - - - - - - - - - - - gene.based。表< - makeGeneTable (featureBasedData统计=“pvalue”)负责人(gene.based.table) # # - - - - - eval = TRUE,警告= FALSE,消息= FALSE,结果=“标记”- - - - - - - - - - - - lrTestBias (gene.based。表,箱线图。宽= 0.3)# # - - - - - eval = TRUE,消息= FALSE,警告= FALSE,结果=“标记”- - - - - - - - - - - - gene.based.table。罗斯福< - makeGeneTable (featureBasedData统计=“罗斯福”)lrTestBias (gene.based.table。罗斯福,箱线图。宽= 0.3)# # - - - - - eval = TRUE,警告= FALSE,消息= FALSE,结果=“标记”- - - - - - - - - - - - - - - -结果。< - runPathwaySplice (genewise调整。表= gene.based.table。罗斯福,基因组= " hg19 " id =“ensGene”,测试。猫= c(“:英国石油公司”),go.size。限制= c(5、30)方法=“让”,use.genes.without。猫= TRUE)头(result.adjusted) # # - - - - - eval = TRUE,警告= FALSE,消息= FALSE,结果=“标记”,fig.align =‘正确的’,fig.height = 13, fig.width = 15 - - - - - enmap < - enrichmentMap(通路。res =结果。调整,n = 7, output.file。dir = tempdir()相似。阈值= 0.5,扩展。因子= 2)# # - - - - - eval = FALSE,消息= FALSE,警告= FALSE, fig.show =“隐藏”- - - - - - - - - - - - # dir.name < -系统。文件(“extdata”,包=“PathwaySplice”) # hallmark.local。路径< - file.path (dir.name h.all.v6.0.symbols.gmt.txt) # hlp < - gmtGene2Cat (hallmark.local。途径,genomeID = " hg19”) # #的结果。< - runPathwaySplice (genewise标志。表= gene.based.table。fdr, # genome = "hg19", # id = "ensGene", # gene2cat = hlp, # go.size.limit = c(5, 100), # method = "Wallenius", # binsize = 20, # use.genes.without.cat = TRUE) ## ----eval=FALSE, message=FALSE, warning=FALSE,results='markup',fig.show='hide'---- # # outKegg2Gmt("hsa", file.path(dir.name, "kegg.gmt.txt")) # # kegg.pathways <- gmtGene2Cat(file.path(dir.name, "kegg.gmt.txt"), # genomeID = "hg19") # # result.kegg <- runPathwaySplice(genewise.table = gene.based.table.fdr, # genome = "hg19", # id = "ensGene", # gene2cat = kegg.pathways, # go.size.limit = c(5, 100), # method = "Wallenius", # use.genes.without.cat = TRUE) # ## ----eval=FALSE---------------------------------------------------------- # dir <- system.file("extdata", package="PathwaySplice") # all.gene.table <- readRDS(file.path(dir, "AllGeneTable.rds")) ## ----eval=FALSE, warning=FALSE, message=FALSE, results='markup', fig.show='hide'---- # res.adj <- runPathwaySplice(genewise.table = all.gene.table, # genome = "hg19", # id = "ensGene", # test.cats = "GO:BP", # go.size.limit = c(5, 30), # method = "Wallenius") # # res.unadj <- runPathwaySplice(genewise.table = all.gene.table, # genome = "hg19", # id = "ensGene", # test.cats = "GO:BP", # go.size.limit = c(5, 30), # method = "Hypergeometric") # compareResults(n.go = 20, # adjusted = res.adj, # unadjusted = res.unadj, # gene.based.table = all.gene.table, # output.dir = tempdir(), # type.boxplot = "Only3") ## ----eval=FALSE,warning=FALSE,message=FALSE,results='markup'------------- # PathwaySplice:::compareResults2(result.hyper, # result.Wall, # result.Sampling, # result.Sampling.200k) #