plateSummary {twoddpcr} | R Documentation

## Counts the number of positives and negatives in an experiment and produces estimates for the number of molecules.

### Description

Takes a collection of classified droplets, each corresponding to a well, and produces a list of positive/negative counts and estimates of how many molecules are in each well.

### Usage

    plateSummary(
      wells,
      ...,
      ch1Label = "Mt",
      ch2Label = "Wt",
      sortByLetter = FALSE
    )

    ## S4 method for signature 'list'
    plateSummary(wells, ch1Label = "Mt", ch2Label = "Wt", sortByLetter = FALSE)

    ## S4 method for signature 'ddpcrPlate'
    plateSummary(
      wells,
      cMethod,
      ch1Label = "Mt",
      ch2Label = "Wt",
      sortByLetter = FALSE
    )

### Arguments

`wells` | Either a `ddpcrPlate` object or a list of data frames, each of which comprises droplet amplitudes and their corresponding classifications in a given well.
`...` | Other options depending on the type of `wells`.
`ch1Label` | The prefix to use for the channel 1 target. Defaults to "Mt".
`ch2Label` | The prefix to use for the channel 2 target. Defaults to "Wt".
`sortByLetter` | If `TRUE`, the resulting data frame is sorted by the letter in the well names first, e.g. "A02" comes before "B01". If `FALSE`, the result is sorted by the numeric component of the well names first, e.g. "B01" comes before "A02". Defaults to `FALSE`.
`cMethod` | The classification method to create a summary for.

### Value

A data frame with droplet counts and molecules number estimates for each well.

### Author(s)

Anthony Chiu, anthony.chiu@cruk.manchester.ac.uk

### Examples

    ## Take a ddpcrPlate object and summarise its wells.
    krasPlate <- ddpcrPlate(KRASdata)
    plateSummary(krasPlate, cMethod="Cluster")

[Package twoddpcr version 1.12.0 Index]