plateClassification {twoddpcr} | R Documentation

## Set and retrieve classifications for multiple wells.

### Description

Retrieve multiple classification factors that have been assigned to a `ddpcrPlate` object.

### Usage

    plateClassification(
      theObject,
      cMethod = NULL,
      withAmplitudes = FALSE,
      wellCol = FALSE
    )

    ## S4 method for signature 'ddpcrPlate'
    plateClassification(
      theObject,
      cMethod = NULL,
      withAmplitudes = FALSE,
      wellCol = FALSE
    )

    plateClassification(theObject, cMethod) <- value

    ## S4 replacement method for signature 'ddpcrPlate,character,list'
    plateClassification(theObject, cMethod) <- value

    ## S4 replacement method for signature 'ddpcrPlate,character,factor'
    plateClassification(theObject, cMethod) <- value

### Arguments

`theObject` | A `ddpcrPlate` object.
`cMethod` | This is the name of the classification to retrieve and should be a character vector. If `NULL`, then all of the classifications are obtained. Defaults to `NULL`.
`withAmplitudes` | If `TRUE`, the droplet amplitudes are included. Defaults to `FALSE`.
`wellCol` | If `TRUE`, an additional column is included in the output, where each entry is the name of the well from which the droplet originated. In this case, this setting forces the `withAmplitudes` parameter to `TRUE`. Defaults to `FALSE`.
`value` | Either: A list of factors, where each item of the list corresponds to a well; A single factor corresponding to all of the wells combined. This should be ordered by the order of the output of the `amplitudes` function when the rows of the data frames have been bound together, i.e. with `do.call(rbind, amplitudes(theObject))`.

### Value

If requesting one classification without the amplitudes, a list of factors corresponding to the classifications is returned. Otherwise, a list of data frames is returned where each row corresponds to a droplet in the corresponding well.

### Author(s)

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

### Examples

    ### The examples here show how this method works by setting classifications
    ### using data frames. To do this, we use the
    ### \code{\link{thresholdClassify}} method on _data frames_. Note that
    ### \code{thresholdClassify} also works directly on \code{ddpcrWell} and
    ### \code{ddpcrPlate} objects; this is simply an illustration of
    ### how to use the \code{plateClassification} method directly. In general,
    ### it is recommended to use \code{thresholdClassify} directly on
    ### \code{ddpcrPlate} objects.

    ## Create a ddpcrPlate object.
    krasPlate <- ddpcrPlate(wells=KRASdata)

    ## Classify a data frame of droplets and keep it in a _single_ data frame.
    ## Set the new classification from this.
    droplets <- do.call(rbind, amplitudes(krasPlate))
    clSingle <- thresholdClassify(droplets,
                                  ch1Threshold=7000, ch2Threshold=3500,
                                  fullTable=FALSE)
    plateClassification(krasPlate, "thresholdSing") <- clSingle

    ## We can also set the new classification from a list of factors.
    clList <- lapply(KRASdata, thresholdClassify, ch1Threshold=7000,
                     ch2Threshold=3500, fullTable=FALSE)
    plateClassification(krasPlate, "thresholdList") <- clList

    ## We can get all of the classifications as a list of data frames.
    plate <- plateClassification(krasPlate)
    lapply(plate, head, n=1)

    ## We can include the droplet amplitudes columns.
    plate <- plateClassification(krasPlate, withAmplitudes=TRUE)
    lapply(plate, head, n=1)

    ## We can focus on specific classifications.
    plate <- plateClassification(krasPlate, cMethod=c("thresholdSing",
                                                      "thresholdList"))
    lapply(plate, head, n=1)

    ## The wellCol option adds an extra column showing which well the droplet
    ## came from.
    plate <- plateClassification(krasPlate, withAmplitudes=TRUE, wellCol=TRUE)
    lapply(plate, head, n=1)

[Package twoddpcr version 1.12.0 Index]