## ----global_options, include=FALSE-------------------------------------------- knitr::opts_chunk$set(warning = FALSE, message = FALSE, eval = FALSE, fig.width = 7, fig.height = 4.2) ## ----load_libraries, results='hide'------------------------------------------- # library(RCAS) ## ----------------------------------------------------------------------------- # FUS_rep1_path <- system.file('extdata', 'FUS_Nakaya2013c_hg19.bed', package = 'RCAS') # FUS_rep2_path <- system.file('extdata', 'FUS_Nakaya2013d_hg19.bed', package = 'RCAS') # FMR1_rep1_path <- system.file('extdata', 'FMR1_Ascano2012a_hg19.bed', package = 'RCAS') # FMR1_rep2_path <- system.file('extdata', 'FMR1_Ascano2012b_hg19.bed', package = 'RCAS') # EIF4A3_rep1_path <- system.file('extdata', 'EIF4A3Sauliere20121a.bed', package = 'RCAS') # EIF4A3_rep2_path <- system.file('extdata', 'EIF4A3Sauliere20121b.bed', package = 'RCAS') ## ----------------------------------------------------------------------------- # 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') # write.table(projData, projDataFile, sep = '\t', quote =FALSE, row.names = FALSE) ## ----------------------------------------------------------------------------- # gtfFilePath <- system.file("extdata", "hg19.sample.gtf", package = "RCAS") ## ----------------------------------------------------------------------------- # databasePath <- file.path(getwd(), 'myProject.sqlite') # invisible(createDB(dbPath = databasePath, projDataFile = projDataFile, gtfFilePath = gtfFilePath, genomeVersion = 'hg19')) ## ----------------------------------------------------------------------------- # RCAS::deleteSampleDataFromDB(dbPath = databasePath, sampleNames = c('FMR1_1', 'FMR1_2')) ## ----------------------------------------------------------------------------- # knitr::kable(RCAS::summarizeDatabaseContent(dbPath = databasePath)) ## ----------------------------------------------------------------------------- # 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('FUS', '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'))