class-illuminaChannel: Class "illuminaChannel"

In markdunning/beadarray-devel: Quality assessment and low-level analysis for Illumina BeadArray data

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")

markdunning/beadarray-devel documentation built on May 21, 2019, noon