plotBeadIntensities: Plotting the intensities of selected beads on a section

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

Description

The function will plot the intensities of selected beads on a specified array

Usage

plotBeadIntensities(BLData, array = 1, BeadIDs, transFun = logGreenChannelTransform, cols = NULL, ...)

Arguments

BLData	a beadLevelData object
array	numeric specifying which array to plot the intensities from
BeadIDs	what ArrayAddress IDs to be plotted
transFun	function specifying what transformation to be applied to the beadLevelData prior to plotting
cols	a vector of colours to be used to plot each ID. If NULL the rainbow function is used to generate colours.
...	other argument that may be passed along to plot.

Details

The function will take all data from the specified section, apply the transformation (the default is to do log2) and then find the subset of beads that have the specified ID. These IDs should match the numeric ArrayAddress IDs that are stored in the beadLevelData object.

Value

Plot is produced on current graphical device.

Author(s)

Mark Dunning

Examples

if(require(beadarrayExampleData)){


data(exampleBLData)

randIDs = sample(getBeadData(exampleBLData, array=1, what="ProbeID"),10)

plotBeadIntensities(exampleBLData, array=1, BeadIDs = randIDs)

}

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