add.lines	MANOR-internal
amplicon.flag	flags
arrayCGH2txt	MANOR-internal
arrayTrend	arrayTrend
arrayTrend.arrayCGH	arrayTrend
arrayTrend.default	arrayTrend
center	MANOR-internal
check.names	MANOR-internal
chrom	MANOR-internal
chromosome.flag	flags
clone.qscore	qscores
control.flag	flags
cv	MANOR-internal
dapi.snr.flag	flags
detectSB	detectSB
detectSB.arrayCGH	detectSB
detectSB.default	detectSB
dyn.x.qscore	qscores
dyn.y.qscore	qscores
dynamics.qscore	qscores
edge	spatial
edge.norm	spatial
edge.txt	spatial
flag	flag.arrayCGH
flag.aggregate.arrayCGH	MANOR-internal
flag.arrayCGH	flag.arrayCGH
flag.summary	flag.summary
flag.summary.arrayCGH	flag.summary
flag.summary.default	flag.summary
flags	flags
genome.plot	genome.plot
genome.plot.arrayCGH	genome.plot
genome.plot.default	genome.plot
getChromosomeArm	MANOR-internal
global.spatial.flag	flags
gradient	spatial
gradient.gpr	spatial
gradient.norm	spatial
html.report	html.report
html.report.arrayCGH	html.report
html.report.default	html.report
import	import
import.default.aux	import
import.gpr.aux	import
import.spot.aux	import
intensity.flag	flags
intensity.plot	MANOR-internal
local.spatial.flag	flags
MANOR	norm
manor	norm
MANOR-internal	MANOR-internal
my.aggregate.data.frame	MANOR-internal
nem	nem
nem.arrayCGH	nem
nem.default	nem
norm	norm
norm.arrayCGH	norm
num.chromosome.flag	MANOR-internal
pct.clone.qscore	qscores
pct.replicate.qscore	qscores
pct.spot.before.qscore	qscores
pct.spot.qscore	qscores
position.flag	flags
print.flag	MANOR-internal
qscore	qscore
qscore.arrayCGH	qscore.arrayCGH
qscore.summary	qscore.summary
qscore.summary.arrayCGH	qscore.summary
ref.snr.flag	flags
rename	MANOR-internal
rep.flag	flags
replicate.aux	MANOR-internal
replicate.flag	flags
report.plot	report.plot
report.plot.arrayCGH	report.plot
report.plot.default	report.plot
smoothness.qscore	qscores
SNR.flag	flags
sort	sort
sort.arrayCGH	sort
spatial	spatial
spatial.flag	flags
spot.corr.flag	MANOR-internal
spot.flag	flags
to.flag	to.flag
to.qscore	qscore
unique.flag	flags
val.mark.flag	flags
var.replicate.qscore	qscores
w	MANOR-internal
