ExomeCNV-package	ExomeCNV-package
calculate.logR	calculate.logR
chr.hash	chr.hash
chr.median	calculate.logR
classify.eCNV	classify.eCNV
classify.logR	classify.eCNV
CNV.analyze	CNV.analyze
cnv.points	do.plot.eCNV
colors	colors
combine.baf	multi.LOH.analyze
combine.CNV	combine.CNV
combine.LOH	multi.LOH.analyze
COVERAGE_HEADER	colors
do.DNAcopy	multi.LOH.analyze
do.merge.cnv.intervals	combine.CNV
do.merge.loh.intervals	multi.LOH.analyze
do.plot.eCNV	do.plot.eCNV
do.plot.loh	do.plot.loh
do.plot.one.eCNV	do.plot.eCNV
do.plot.one.loh	do.plot.loh
ExomeCNV	ExomeCNV-package
expand.loh	expand.loh
find.max.of.2lists	pool.coverage
find.min.of.2lists	LOH.analyze
get.alpha	get.AUC
get.alpha.inv	get.AUC
get.AUC	get.AUC
get.end.position	LOH.analyze
get.power	get.AUC
get.power.inv	get.AUC
get.proper.cnv.positions	CNV.analyze
get.r.cutoff	classify.eCNV
get.sensitivity	get.AUC
get.specificity	get.AUC
good.percent	colors
guesstimate.contamination	guesstimate.contamination
guesstimate.contarmination	guesstimate.contamination
LOH.analyze	LOH.analyze
make.chunk	combine.CNV
make.loh.chunk	multi.LOH.analyze
make.loh.strata	multi.LOH.analyze
MIL	colors
multi.CNV.analyze	multi.CNV.analyze
multi.LOH.analyze	multi.LOH.analyze
my.cols	combine.CNV
normalize.logR	calculate.logR
one.sample.loh.test	LOH.analyze
phalfnorm	LOH.analyze
pool.coverage	pool.coverage
pool.coverage.from.files	pool.coverage
r.cutoffs	colors
RBIND_LIM	colors
read.all.coverage	read.all.coverage
read.coverage.gatk	read.coverage.gatk
read.coverage.gtf	read.coverage.gtf
read.eCNV	read.eCNV
read.gtf	read.coverage.gtf
rho.list	colors
save.logR	save.logR
strip.chr.name	CNV.analyze
test.num.copy	colors
two.sample.loh.CMH.test	LOH.analyze
two.sample.loh.deviation.test	LOH.analyze
two.sample.loh.test	LOH.analyze
window.sizes	colors
write.loh.output	write.loh.output
write.output	write.output
