backgroundCorrectSingleSection: Background correct an array-section

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

Description

Function to perform a basic bead-level background correction using a defined set of foreground and background intensities.

Usage

backgroundCorrectSingleSection(BLData, array = 1, fg="Grn", bg="GrnB", newName = "Grn.bc")

Arguments

BLData	a beadLevelData object
array	the number of the array-section to be corrected
fg	the name under which the foreground intensities are stored
bg	the name under which the background intensities are stored
newName	Name to store the corrected intensities

Details

This function takes two attributes of a bead-level object and returns that bead-level object with an additional attribute consisting of the difference of the other two. We anticipate this being used as a simple background correction step, returning the difference between foreground and background intensities to be used as the specific intensity associated with a bead.

Functions to perform more advanced background correction steps can easily be constructed after consideration of this function.

Value

beadLevelData object with modified beadData slot for the particular section

Author(s)

Mark Dunning

Examples

## Not run: 

if(require(beadarrayExampleData)){

  data(exampleBLData)

  head(exampleBLData[[1]])

  for(i in 1:2){
	  exampleBLData = backgroundCorrectSingleSection(exampleBLData, array=i)
  }


  head(exampleBLData[[1]])

  } else {
  
  stop("You will need the beadarrayExampleData package to run this example")
}


## End(Not run)

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