runReportMetaAnalysis {RCAS} | R Documentation |
Generate a stand-alone HTML report with interactive figures and tables from a pre-calculated RCAS database (using RCAS::createDB) to compare multiple samples.
runReportMetaAnalysis(dbPath = "RCAS.sqlite", sampleTablePath, outDir = getwd(), outFile = NULL, quiet = FALSE, selfContained = TRUE)
dbPath |
Path to the sqlite database generated by RCAS::createDB |
sampleTablePath |
A tab-separated file with two columns (no rownames) header 1: sampleName, header 2: sampleGroup |
outDir |
Path to the output directory. (default: current working directory) |
outFile |
Name of the output HTML report (by default, the base name of sampleTablePath value is used to create a name for the HTML report) |
quiet |
boolean value (default: FALSE). If set to TRUE, progress bars and chunk labels will be suppressed while knitting the Rmd file. |
selfContained |
boolean value (default: TRUE). By default, the generated html file will be self-contained, which means that all figures and tables will be embedded in a single html file with no external dependencies (See rmarkdown::html_document) |
An html generated using rmarkdown/knitr/pandoc that contains interactive figures, tables, and text that provide an overview of the experiment
dbPath <- system.file("extdata", "hg19.RCASDB.sqlite", package='RCAS') #Hint: use RCAS::summarizeDatabaseContent to see which samples have processed #data in the database. summarizeDatabaseContent(dbPath = dbPath) #Create a data table for samples and their groups sampleGroup field is used #to group replicates of #the same sample into one group in visualizations. #Any arbitrary name can be used for sampleGroup field. However, entries in #the sampleName field must be available in the queried database sampleData <- data.frame('sampleName' = c('FUS', 'FMR1'), 'sampleGroup' = c('FUS', 'FMR1'), stringsAsFactors = FALSE) write.table(sampleData, 'sampleDataTable.tsv', sep = '\t', quote =FALSE, row.names = FALSE) #Use the generated database to run a report runReportMetaAnalysis(dbPath = 'hg19.RCASDB.sqlite', sampleTablePath = 'sampleDataTable.tsv')