runReportMetaAnalysis {RCAS} | R Documentation

## runReportMetaAnalysis

### Description

Generate a stand-alone HTML report with interactive figures and tables from a pre-calculated RCAS database (using RCAS::createDB) to compare multiple samples.

### Usage

    runReportMetaAnalysis(
      dbPath = "RCAS.sqlite",
      sampleTablePath,
      outDir = getwd(),
      outFile = NULL,
      quiet = FALSE,
      selfContained = TRUE
    )

### Arguments

`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)

### Value

An html generated using rmarkdown/knitr/pandoc that contains interactive figures, tables, and text that provide an overview of the experiment

### Examples

    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')

[Package RCAS version 1.16.0 Index]