ChIPseqR-package	ChIPseqR-package
$,ReadCounts-method	ReadCounts
$<-,ReadCounts,ANY-method	ReadCounts
$<-,ReadCounts-method	ReadCounts
.plotReads	plotReads
.plotWindow	plotWindow
alignFeature	alignFeature
allGroups	internal
allWords	internal
as.data.frame,BindScore-method	BindScore
binding	accessors
binding,ANY-method	accessors
binding,BindScore-method	BindScore
binding-methods	accessors
BindScore	BindScore
BindScore-class	BindScore
callBindingSites	callBindingSites
callBindingSites,ANY-method	callBindingSites
callBindingSites,character-method	callBindingSites
callBindingSites,matrix-method	callBindingSites
callBindingSites,ReadCounts-method	callBindingSites
callBindingSites-methods	callBindingSites
ChIPseqR	ChIPseqR-package
chrLength	ReadCounts
chrLength,BindScore-method	BindScore
chrLength,ReadCounts-method	ReadCounts
chrLength,RLEReadCounts-method	RLEReadCounts-class
compress	compress-methods
compress,BindScore-method	compress-BindScore
compress,ReadCounts-method	compress-ReadCounts
compress,RLEBindScore-method	compress-methods
compress,RLEReadCounts-method	compress-methods
compress-BindScore	compress-BindScore
compress-methods	compress-methods
cutoff	accessors
cutoff,ANY-method	accessors
cutoff,BindScore-method	BindScore
cutoff-methods	accessors
cutoff<-	accessors
cutoff<-,ANY-method	accessors
cutoff<-,BindScore-method	BindScore
cutoff<--methods	accessors
decompress	decompress
decompress,ANY-method	decompress-methods
decompress,Rle-method	decompress-methods
decompress,RLEBindScore-method	decompress
decompress,RleList-method	decompress-methods
decompress,RLEReadCounts-method	decompress
decompress-methods	decompress-methods
diNucTest	internal
exportBindSequence	exportBindSequence
getBindCor	getBindCor
getBindLen	getBindLen
getCutoff	getCutoff
head,BindScore-method	BindScore
lapply,BindScore-method	BindScore
lapply,ReadCounts-method	ReadCounts
length,BindScore-method	BindScore
length,ReadCounts-method	ReadCounts
length<-,BindScore-method	BindScore
length<-,ReadCounts-method	ReadCounts
max,BindScore-method	BindScore
min,BindScore-method	BindScore
names,BindScore-method	BindScore
names,ReadCounts-method	ReadCounts
names<-,BindScore,ANY-method	BindScore
names<-,ReadCounts,ANY-method	ReadCounts
nreads	ReadCounts
nreads,ReadCounts-method	ReadCounts
nreads,RLEReadCounts-method	RLEReadCounts-class
nullDist	accessors
nullDist,ANY-method	accessors
nullDist,BindScore-method	BindScore
nullDist-methods	accessors
nullDist<-	accessors
nullDist<-,ANY-method	accessors
nullDist<-,BindScore-method	BindScore
nullDist<--methods	accessors
oligoNucTest	internal
peaks	accessors
peaks,ANY-method	accessors
peaks,BindScore-method	BindScore
peaks-methods	accessors
pickPeak	pickPeak
plot,BindScore,missing-method	plot-BindScore
plot,ReadCounts,missing-method	plot-ReadCounts
plot,RLEReadCounts,missing-method	plot-ReadCounts
plotBind	internal
plotFreq	internal
pos2gff	pos2gff
pvalue	accessors
pvalue,ANY-method	accessors
pvalue-methods	accessors
range,BindScore-method	BindScore
ReadCounts	ReadCounts
ReadCounts-class	ReadCounts
RLEBindScore-class	RLEBindScore-class
RLEReadCounts-class	RLEReadCounts-class
sapply,ReadCounts-method	ReadCounts
score	accessors
score,BindScore-method	BindScore
simpleNucCall	simpleNucCall
startScore	startScore
strandPileup	strandPileup
strandPileup,AlignedRead-method	strandPileup
strandPileup,data.frame-method	strandPileup
strandPileup-methods	strandPileup
support	accessors
support,ANY-method	accessors
support,BindScore-method	BindScore
support-methods	accessors
tail,BindScore-method	BindScore
triNucTest1	internal
triNucTest2	internal
views2nucFreq	internal
windowCounts	windowCounts
[,BindScore,ANY,missing,missing-method	BindScore
[,ReadCounts,ANY,missing,missing-method	ReadCounts
[<-,ReadCounts,ANY,missing,ANY-method	ReadCounts
[<-,ReadCounts,ANY,missing-method	ReadCounts
[[,BindScore,ANY,missing-method	BindScore
[[,BindScore,ANY,numeric-method	BindScore
[[,ReadCounts,ANY,missing-method	ReadCounts
[[<-,ReadCounts,ANY,missing,ANY-method	ReadCounts
[[<-,ReadCounts,ANY,missing-method	ReadCounts
