extractBadProbes {crosshybDetector}R Documentation

Extract corruptor and corrupted probes

Description

This function extracts the corruptor and corrupted probes for each channel from the output of crosshyb

Usage

extractBadProbes(input, pVal = 0.001)

Arguments

input the output of crosshyb
pVal if the pvalue of a probe is < pVal, the probe is flagged as corruptor

Value

A list containing:

corruptorsR index of probes flagged as corruptors based on red channel intensity
corruptedR index of probes flagged as corrupted based on red channel intensity
corruptorsG index of probes flagged as corruptors based on green channel intensity
corruptedG index of probes flagged as corrupted based on green channel intensity
corruptorsRG index of probes flagged as corruptors based on red AND green channel intensities - intersection of corruptorsR with corruptorsG
corruptedRG index of probes flagged as corrupted based on red AND green channel intensities - intersection of corruptedR with corruptedG

Author(s)

Paolo Uva

See Also

crosshyb

Examples

## Not run: 
# Run crosshyb algorithm...
# This function will take several minutes to finish
data(raw)
data(probeSeq)
crosshyb.out <- crosshyb(raw, probeSeq, plate=1, numPermut=10000,
                         probeNameID="Name", probes=c("probes", "spike"),
                         satValue = 65535, maxProbes=100)                      
## End(Not run)

# ... or load directly the crosshyb output
data(crosshyb.out)

# Extract bad probes
badProbes <- extractBadProbes(crosshyb.out, pVal=0.01)


[Package crosshybDetector version 1.0.4 Index]