Description Details See Also Examples

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).

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.

`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`

1 2 3 4 5 | ```
## Not run:
plate <- new_plate(sample_data_dir(), type = plate_types$pnpp_experiment)
type(plate)
## End(Not run)
``` |

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