| extractBadProbes {crosshybDetector} | R Documentation |
This function extracts the corruptor and corrupted probes for each channel
from the output of crosshyb
extractBadProbes(input, pVal = 0.001)
input |
the output of crosshyb |
pVal |
if the pvalue of a probe is < pVal, the probe is flagged as corruptor |
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 |
Paolo Uva
## 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)