alevinQCShiny {alevinQC}R Documentation

Generate alevin summary shiny app

Description

Generate a shiny app summarizing the main aspects of an alevin quantification run. The app generation assumes that alevin has been run with the –dumpFeatures flag to generate the necessary output files.

Usage

alevinQCShiny(baseDir, sampleId, customCBList = list())

Arguments

baseDir

Path to the output directory from the alevin run (should be the directory containing the alevin directory).

sampleId

Sample ID, will be used set the title for the app.

customCBList

Named list with custom set(s) of barcodes to provide summary statistics/plots for, in addition to the whitelists generated by alevin.

Value

A shiny app.

Author(s)

Charlotte Soneson

Examples

app <- alevinQCShiny(baseDir = system.file("extdata/alevin_example_v0.14",
                                           package = "alevinQC"),
                     sampleId = "example")
if (interactive()) {
    shiny::runApp(app)
}


[Package alevinQC version 1.9.0 Index]