Panel settings

Panel settings describe how the pools in a Mad4hatter run map onto multiplex PCR reactions, and which targets should be left out of QC calculations (they are still kept in the filtered allele outputs).

Usage

panel_settings(
  pool_reactions = character(),
  excluded_targets = character(),
  base = NULL
)

Arguments

pool_reactions

Named character vector mapping pool names (as passed to Mad4hatter's --pools) to reaction labels, e.g. c(D1 = "1", R1 = "1", R2 = "2").

excluded_targets

Character vector of target names to exclude from QC calculations.

base

Optional panel settings to extend. Pools in pool_reactions override those in base, and excluded_targets are added to those in base.

Value

An object of class ampseqQC_panel_settings.

Details

The pools present in a run are always taken from the pool column of panel_information/amplicon_info.tsv; the settings only need to know which reaction each pool was amplified in. Pools can be supplied in any combination or subset.

Examples

# Run R1.2 in its own reaction instead of alongside D1
panel_settings(c(R1 = "3", R1.2 = "3"), base = default_panel_settings())
#> <ampseqQC panel settings>
#> Pool -> reaction:
#>   1: D1, D1.1, 1A, R1.1, 1B, 5, M1, M1.1, M1.addon
#>   2: R2, R2.1, 2, M2, M2.1
#>   3: R1, R1.2
#> Targets excluded from QC: 14 

# A bespoke panel
panel_settings(c(poolA = "A", poolB = "B"))
#> <ampseqQC panel settings>
#> Pool -> reaction:
#>   A: poolA
#>   B: poolB
#> Targets excluded from QC: 0