showArrayMask: Show Array Mask

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

Description

Function to display beads masked by BASH. The masked beads are assumed to have a weight of 0 in the specified weights column.

Usage

showArrayMask(BLData,array = 0, override = FALSE, wtsName = "wts", transFun = logGreenChannelTransform, outlierFun = illuminaOutlierMethod, horizontal=TRUE)

Arguments

BLData	A BeadLevelList object.
override	Logical. Plotting a large mask can cause slowdown problems. By default, if more than 200 000 beads are masked, the current mask will not be plotted. You can force the mask to be plotted by setting this argument to TRUE, however beware as this may cause slower systems to freeze.
wtsName	name under which the bead weights are stored
array	numeric index of the array to plot
transFun	function to transform intensities prior to calculating outliers
outlierFun	function to remove outliers
horizontal	if TRUE the resulting image is plotting with the longest edge along the x axis

Details

showArrayMask plots the beads on an array that have been assigned a weight of 0 by BASH in red, and beads determined to be outliers in black.

Value

None returned

Author(s)

Jonathan Cairns and Mark Dunning

Examples

if(require(beadarrayExampleData)){

  data(exampleBLData)

  showArrayMask(exampleBLData,2)

}

beadarray documentation built on Nov. 8, 2020, 4:51 p.m.