addFeatureData: Add probe data

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

Description

Adds extra probe-specific data to an ExpressionSetIllumina object.

Usage

addFeatureData(data, toAdd = c("SYMBOL", "PROBEQUALITY", "CODINGZONE", "PROBESEQUENCE"), annotation = NULL)

Arguments

data	An ExpressionSetIllumina object
toAdd	Either a pre-prepared data frame, or characters which refer to mappings within an annotation pacakge
annotation	Optional character identifying the annotation of the ExpressionSetIllumina object. e.g. Humanv3, Mousev2.

Details

The function will identify which package should be used by concatenating illumina with the value of the annotation slot of the object, or the annotation argument passed in. If this package is not installed on the users computer, then the function will fail.

Assuming the package has been correctly loaded, the character vector toAdd is converted to the names of environments within the package. These environments are then queried with the featureNames of the input object. The result of each query is converted to a data frame and merged with the original feature data of the object.

Alternatively, rather than querying from an annotation pacakge, a pre-prepared data frame can be used.

Value

An ExpressionSetIllumina object with modified featureData

Examples

if(require(beadarrayExampleData)){

data(exampleSummaryData)

exampleSummaryData <- addFeatureData(exampleSummaryData)

}

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