Read alevin-fry data required to generate summary report

Read all alevin-fry output files required to generate the summary report or shiny app.

readAlevinFryQC(mapDir, permitDir, quantDir)

Arguments

mapDir

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

permitDir

Path to the output directory from the generate-permit-list and collate runs.

quantDir

Path to the output directory from the alevin-fry quant run (should be the directory containing the alevin folder).

Value

A list collecting all necessary information for generating the summary report/shiny app.

Author

Charlotte Soneson

Examples

alevinfry <- readAlevinFryQC(
    mapDir = system.file("extdata/alevinfry_example_v0.5.0/map",
                         package = "alevinQC"),
    permitDir = system.file("extdata/alevinfry_example_v0.5.0/permit",
                            package = "alevinQC"),
    quantDir = system.file("extdata/alevinfry_example_v0.5.0/quant",
                           package = "alevinQC"))