wellClassification {twoddpcr}R Documentation

Retrieve a classification vector.

Description

Retrieve the classification from a ddpcrWell object.

Usage

wellClassification(theObject, cMethod = NULL, withAmplitudes = FALSE)

## S4 method for signature 'ddpcrWell'
wellClassification(theObject, cMethod = NULL,
  withAmplitudes = FALSE)

wellClassification(theObject, cMethod) <- value

## S4 replacement method for signature 'ddpcrWell'
wellClassification(theObject, cMethod) <- value

Arguments

theObject

A ddpcrWell object.

cMethod

The names (or column numbers) of the classification to retrieve. If NULL, then all of the classifications are obtained. Defaults to NULL when retrieving. When setting a classification, this cannot be NULL.

withAmplitudes

Logical value. If TRUE, returns a data frame with the droplet amplitudes and corresponding classifications. If FALSE, returns the classification vector only. Defaults to FALSE.

value

A factor with the same length as the number of droplets in theObject, with levels in ddpcr$classesRain.

Value

A factor or data frame corresponding to the requested classification(s).

Author(s)

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

See Also

wellClassificationMethod for the name of the classification method.

Examples

## Take some droplets with a given classification.
amplitudes <- KRASdata[["E03"]][, c("Ch1.Amplitude", "Ch2.Amplitude")]

## Create a ddpcrWell object with the amplitudes only.
aWell <- ddpcrWell(well=amplitudes)

## This has no classification yet.
head(wellClassification(aWell))

## We check the classification now, showing the amplitudes as well.
head(wellClassification(aWell, withAmplitudes=TRUE))

## Now set a sample classification.
wellClassification(aWell, cMethod="Sample") <-
  rep(c("NN", "NP", "PN", "PP"), numDroplets(aWell) / 4)
head(wellClassification(aWell, withAmplitudes=TRUE))
[Package twoddpcr version 1.11.0 Index]