crosshybImage {crosshybDetector} | R Documentation |
Draws an image with the spatial distribution on the array of probes flagged as corruptors or corrupted.
crosshybImage(raw, plate, parent, children, arrayName, channel = c("red", "green"), doPlot = FALSE)
raw |
an object of class marrayRaw |
plate |
the plate number |
parent |
a vector of probe numbers corresponding to the corruptor probes |
children |
a vector of probe numbers corresponding to the corrupted probes |
arrayName |
the name of the array. Used to create the output file name |
channel |
the channel to use for drawing image |
doPlot |
logical, if TRUE writes the image to file |
This function creates an image with the spatial distribution of the corruptor
and corrupted probes on the array for the selected channel. If doPlot
is TRUE, the image is
written to a file and nothing is displayed. The color intensity of corrupted probes is proportional
to the intensity value
Paolo Uva
data(raw) data(probeSeq) ## Not run: # Run crosshyb... # This function will take several minutes to finish crosshyb.out <- crosshyb(raw, probeSeq, plate=1, numPermut=10000, name="Name", probes=c("probes", "spike"), satValue = 65535, maxProbes=100) ## End(Not run) # ... or load directly crosshyb output data(crosshyb.out) # Extract corrupted and corruptor probes badprobes <- extractBadProbes(crosshyb.out, pVal=0.01) # Write results for RED channel if(length(badprobes$corruptorsR)){ parent <- badprobes$corruptorsR child <- badprobes$corruptedR crosshybImage(raw, plate = 1, parent=parent, children=child, arrayName = "myArray", channel="red", doPlot=FALSE) }