annotationInterface: Storage of annotation information

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

Description

An interface to set or retrieve information about the annotation of a beadLevelData or ExpressionSetIllumina object.

Usage

    suggestAnnotation(data,verbose=FALSE)
    annotation(object,...)

Arguments

data	An object of class beadLevelData-class

.

verbose	If TRUE, report overlaps with known platforms
object	Either a beadLevelData-class or ExpressionSetIllumina-class
...	Extra arguments used by annotation

Details

A character string is used to specify the annotation with the currently supported values being; Humanv4, Humanv3, Humanv2, Humanv1, Mousev2, Mousev1, Mousev1p1 and Ratv1. This string is used within beadarray to retrieve control probe IDs within particular QC functions.

The suggestAnnotation function tries to determine a suitable value for a beadLevelData-class based on the probe IDs and compiled list of IDs from all expression platforms. This is based on the percentage of IDs on the array that overlap with IDs from known platforms. The platform with highest overlap is chosen.

Author(s)

Mark Dunning

Examples

if(require(beadarrayExampleData)){

data(exampleBLData)

annotation(exampleBLData)

suggestAnnotation(exampleBLData,verbose=TRUE)

annotation(exampleBLData) <- "Humanv2"
 

data(exampleSummaryData)

annotation(exampleSummaryData)

annotation(exampleBLData) <- "Humanv1"

}

markdunning/beadarray documentation built on May 9, 2019, 8:35 a.m.