readAlevinFryQC: Read alevin-fry data required to generate summary report

In csoneson/alevinQC: Generate QC Reports For Alevin Output

Read alevin-fry data required to generate summary report

Description

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

Usage

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(s)

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"))

csoneson/alevinQC documentation built on Dec. 16, 2024, 6:14 p.m.