plateSummary: Counts the number of positives and negatives in an experiment...

In CRUKMI-ComputationalBiology/twoddpcr: Classify 2-d Droplet Digital PCR (ddPCR) data and quantify the number of starting 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, [e-mail]

Examples

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

CRUKMI-ComputationalBiology/twoddpcr documentation built on Feb. 14, 2021, 9:18 p.m.