beadarray (version 2.22.2)

showArrayMask: Show Array Mask

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

Value

None returned

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.

Examples

if(require(beadarrayExampleData)){

  data(exampleBLData)

  showArrayMask(exampleBLData,2)

}