crosshybImage {crosshybDetector}R Documentation

Spatial distribution of corruptor and corrupted probes

Description

Draws an image with the spatial distribution on the array of probes flagged as corruptors or corrupted.

Usage

crosshybImage(raw, plate, parent, children, arrayName,
              channel = c("red", "green"), doPlot = FALSE)

Arguments

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

Value

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

Author(s)

Paolo Uva

See Also

extractBadProbes

Examples

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)
}


[Package crosshybDetector version 1.0.4 Index]