pnpp_experiment {ddpcr}

Plate type: PNPP experiment

Description

PNPP stands for "Positive-Negative;Positive-Positive", which is a reflection of the clusters of non-empty droplets in the wells. Use this plate type when your ddPCR data has three main clusters: double-negative (FAM-HEX-; empty droplets), double-positive (FAM+HEX+; represent the "PP" in PNPP), and singly-positive (either FAM+HEX- or HEX+FAM-; represent the "NP" in PNPP).

Details

Every pnpp_experiment plate must define which dimension is its positive dimension. The positive dimension is defined as the dimension that corresponds to the dye that has a high fluoresence intensity in all non-empty droplets. The other dimension is defined as the variable dimension. For example, assuming the HEX dye is plotted along the X axis and the FAM dye is along the Y axis, a FAM+/FAM+HEX+ plate will have "Y" as its positive dimension because both non-empty clusters have FAM+ droplets. Similarly, a HEX+/FAM+HEX+ plate will have "X" as its positive dimension.

The positive dimension must be set in order to use a pnpp_experiment. It is not recommended to use this type directly; instead you should use one of the subtypes (fam_positive_pnpp or hex_positive_pnpp). If you do use this type directly, you must set the positive dimension with positive_dim.

Plates with this type have the following analysis steps: INITIALIZE, REMOVE_FAILURES, REMOVE_OUTLIERS, REMOVE_EMPTY, CLASSIFY, RECLASSIFY.

Plates with this type have the following droplet clusters: UNDEFINED, FAILED, OUTLIER, EMPTY (double-negative), RAIN, POSITIVE, NEGATIVE.

See the README for more information on plate types.

See Also

plate_types
fam_positive_pnpp
hex_positive_pnpp
wildtype_mutant_pnpp
positive_dim
wells_positive
wells_negative
analyze
remove_failures
remove_outliers
remove_empty
classify_droplets
reclassify_droplets

Examples

## Not run: 
plate <- new_plate(sample_data_dir(), type = plate_types$pnpp_experiment)
type(plate)

## End(Not run)