# #——global_options,包括= FALSE --------------------------------------- 美元knitr: opts_chunk集(警告= FALSE,消息= FALSE, eval = FALSE, fig.width = 7, fig.height = 4.2) # #——load_libraries,结果= '隐藏 '-------------------------------------- # 库(rca ) ## ------------------------------------------------------------------------ # FUS_rep1_path < -系统。文件(“extdata”、“FUS_Nakaya2013c_hg19。， package = 'RCAS') # FUS_rep2_path <-系统。文件(“extdata”、“FUS_Nakaya2013d_hg19。， package = 'RCAS') # FMR1_rep1_path <-系统。文件(“extdata”、“FMR1_Ascano2012a_hg19。， package = 'RCAS') # FMR1_rep2_path <-系统。文件(“extdata”、“FMR1_Ascano2012b_hg19。'， package = 'RCAS') # EIF4A3_rep1_path <-系统。文件(“extdata”、“EIF4A3Sauliere20121a。'， package = 'RCAS') # EIF4A3_rep2_path <- system. system. system. system. system。文件(“extdata”、“EIF4A3Sauliere20121b。床上,包= rca ') ## ------------------------------------------------------------------------ # projData < - data.frame(“sampleName”= c(‘FUS_1’,‘FUS_2’,‘FMR1_1’,‘FMR1_2’,‘EIF4A3_1’,‘EIF4A3_2’),#“bedFilePath”= c (FUS_rep1_path、FUS_rep2_path # FMR1_rep1_path、FMR1_rep2_path # EIF4A3_rep1_path, EIF4A3_rep2_path), # stringsAsFactors = FALSE) # # projDataFile < - file.path (getwd (), myProjDataFile.tsv) #写。表(projData projDataFile, 9 = \ t,引用= FALSE, row.names = FALSE ) ## ------------------------------------------------------------------------ # gtfFilePath < -系统。文件(“extdata”、“hg19.sample。gtf”,包= " rca ") ## ------------------------------------------------------------------------ # databasePath < - file.path开始(getwd (), myProject.sqlite) #看不见(createDB (dbPath = databasePath,开始projDataFile = projDataFile gtfFilePath = gtfFilePath genomeVersion = ' hg19 ')) ## ------------------------------------------------------------------------ # rca: deleteSampleDataFromDB (dbPath = databasePath,开始sampleNames = c(“FMR1_1”,“FMR1_2 ')) ## ------------------------------------------------------------------------ # knitr:: kable (rca: summarizeDatabaseContent (dbPath = databasePath。开始 )) ## ------------------------------------------------------------------------ # mydb < - RSQLite:: dbConnect (RSQLite: SQLite (),databasePath ) ## ------------------------------------------------------------------------ # RSQLite: dbListTables (mydb ) ## ------------------------------------------------------------------------ # annotationSummaries < - RSQLite: dbReadTable (mydb annotationSummaries) # knitr:: kable (annotationSummaries ) ## ------------------------------------------------------------------------ # sampleData < - data.frame(“sampleName”= c(‘FUS_1’,‘FUS_2’,‘EIF4A3_1’,‘EIF4A3_2’),#“sampleGroup”= c(“付”, 'FUS', 'EIF4A3', 'EIF4A3'), # stringsAsFactors = FALSE) # sampleDataFile <- file.path(getwd(), 'mySampleDataTable.tsv') # write.table(sampleData, sampleDataFile, sep = '\t', quote =FALSE, row.names = FALSE) ## ------------------------------------------------------------------------ # runReportMetaAnalysis(dbPath = databasePath, sampleTablePath = sampleDataFile, # outFile = file.path(getwd(), 'myProject.html'))