load_panel: Load panel information

In beadplexr: Analysis of Multiplex Cytometric Bead Assays

Load panel information

Description

The panel information are stored in resources in the package directory and can be loaded by providing a file or panel name, or a search pattern

Usage

load_panel(.file_name = NULL, .panel_name = NULL, .panel_pattern = NULL)

Arguments

.file_name	Character vector giving the name of an external panel info file. See below for the expected components.
.panel_name	Character vector giving the name of the panel. See below for accepted panel names.
.panel_pattern	The pattern to look for. Can be a regular expression.

Details

If an explicit .file_name is given, .panel_name and .panel_pattern are ignored. If no file is given but a .panel_name is, the .panel_pattern i ignored. Only if no .file_name and .panel_name are given, is the .panel_pattern used.

Value

A list

Included panels

• Human Adipokine Panel* (13-plex)

• Human Anti-Virus Response Panel (13-plex)

• Human CD8/NK Panel (13-plex)

• Human Cytokine Panel 2 (13-plex)

• Human Growth Factor Panel (13-plex)

• Human Inflammation Panel (13-plex)

• Human Metabolic Panel 1 (4-plex)

• Human Proinflammatory Chemokine Panel (13-plex)

• Human T Helper Cytokine Panels (13-plex)

• Mouse Anti-Virus Response Panel (13-plex)

• Mouse Cytokine Panel 2 (13-plex)

• Mouse Free Active/Total TGF-b1 Panel (Mouse/Rat) (1-plex)

• Mouse HSC Panel (13-plex)

• Mouse IgE Panel (1-plex)

• Mouse Immunoglobulin Isotyping Panel (6-plex)

• Mouse Inflammation Panel (13-plex)

• Mouse Proinflammatory Chemokine Panel (13-plex)

• Mouse T Helper Cytokine Panels (13-plex)

Example panel file

The panel information files are formatted in YAML. It has three main parts:

• Some general information about the panel - The order of the major bead groups in the forward and side scatter - Analytes, where each bead ID is listed for each major bead group. The bead IDs are further complemented with the name of the analyte and the start concentration of the standard value

The 'Human Th Cytokine Panel (13-plex)' YAML file is found in /resources/legendplex_human_th_cytokine_panel_13-plex.yml of the package directory.

Examples

library(beadplexr)

.panel_name <- "Human T Helper Cytokine Panels (13-plex)"
panel_info <- load_panel(.panel_name = .panel_name)
panel_info$panel_name

.file_name <- system.file("resources",
                          "legendplex_human_cytokine_panel_2_13-plex.yml",
                          package = "beadplexr")
panel_info <- load_panel(.file_name = .file_name)
panel_info$panel_name

panel_info <- load_panel(.file_name = .file_name, .panel_name = .panel_name)
panel_info$panel_name

suppressWarnings(
# The pattern matches several files, which raises a warning
panel_info <- load_panel(.panel_pattern = "panel_2_13-plex")
)
panel_info$panel_name

beadplexr documentation built on July 9, 2023, 5:59 p.m.