outlierplot: Plot outlier locations

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

Description

Function to plot where the outliers are located on a given array

Usage

outlierplot(BLData, array = 1, transFun = logGreenChannelTransform, outlierFun = illuminaOutlierMethod,n=3, wtsname=NULL, horizontal = TRUE, nSegments = NULL, lowOutlierCol = "blue", highOutlierCol = "pink", outlierPch = ".", main = "", ...)

Arguments

BLData	a beadLevelData object
array	the number of the array to plot
transFun	a function defining how to transform the data prior to calculating outliers
outlierFun	function that will identify outliers
n	an indicator of how extreme an observation must be (e.g. how many MADs from the median), to be passed to the function that will identify outliers
wtsname	column name of BLData object containing weights to feed to the outlier function
horizontal	if TRUE the longest edge of the array section will be on the x axis
nSegments	How many segments the section is divided into. If this argument is left as the default value (NULL) the code will attempt to extract this information from the relevant .sdf file. If it can't be found then the segments will not be indicated on the final plot.
lowOutlierCol	what colour to plot outliers below the median
highOutlierCol	what colour to plot outliers above the median
outlierPch	plotting character for the outliers
main	an optional title for the plot
...	additional arguments

Details

The function calls the specified outlier function to determine the outliers on the array and then plots their location. Points are coloured according the intensity of the bead is above or below the median for that bead-type.

Value

plot produced on current graphical device

Author(s)

Mark Dunning and Mike Smith

Examples

if(require(beadarrayExampleData)){

data(exampleBLData)
outlierplot(exampleBLData, array=1, horizontal = FALSE)


}

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