illuminaChannel-class {beadarray} | R Documentation

## Class "illuminaChannel"

### Description

A class to define how illumina bead-level data are summarized

### Details

From beadarray version 2.0 onwards, users are allowed more flexibility in how to create summarized data from bead-level data. The `illuminaChannel` is a means of allowing this flexibility by definining how summarization will be performed on each array section in the bead-level data object. The three keys steps applied to each section are; 1) use a transform function to get the quantities to be summarized (one value per bead). The most common use-case would be to extract the Green channel intensities and possibly perform a log2 transformation. 2) remove any outliers from this list of values 3) split the values according to ArrayAddressIDs and apply the definied `exprFun` and `varFun` to the quantities belonging to each ArrayAddress.

### Slots/List Components

Objects of this class contain the following slots

`transFun`: | function to transform the data from each array-section.
`outlierFun`: | A function for identifying outliers from a list of bead intensiites and associated ArrayAddressIDs .
`exprFun`: | A function for producing a single summary of expression level from a vector of bead-type intensities. e.g. mean .
`varFun`: | A function for producing a single summary of variability from a vector of bead-type intensities. e.g. sd
`name`: | Character vector that defines a name for the channel

### Author(s)

Mark Dunning

### See Also

`summarize`

### Examples

    greenChannel

    redChannel = new("illuminaChannel", redChannelTransform, illuminaOutlierMethod, mean, sd, "R")

    logRatio = new("illuminaChannel", logRatioTransform, illuminaOutlierMethod, mean, sd, "M")

[Package beadarray version 2.37.1 Index]