API for VanillaICE
A Hidden Markov Model for high throughput genotyping arrays

Global functions
"[",ArrayViews,ANY-method	Man page
$,ArrayViews-method	Man page
$<-,ArrayViews-method	Man page
'[',ArrayViews,ANY-method	Man page
.apply_cnv_filters	Source code
.calculateBAFEmission	Source code
.calculateEmission	Source code
.calculateTransitionProbs	Source code
.colnames	Source code
.cytobandColors	Source code
.drawPolygon	Source code
.drawStalk	Source code
.find_xlim_percent	Source code
.firstSegment	Source code
.hmm	Source code
.hmm_states	Source code
.lapply	Source code
.onAttach	Source code
.onUnload	Source code
.parseSourceFile	Source code
.path	Source code
.resolveIndex	Source code
.rownames	Source code
.snp_id_column	Source code
.update_baf	Source code
.xyplotlist	Source code
ArrayViews	Man page Source code
ArrayViews,numeric,numeric-method	Man page
ArrayViews-class	Man page
BAF_ALLELE_NAMES	Source code
BAF_MEANS	Source code
BAF_PRIOR_MEANS	Source code
BAF_SDS	Source code
CN_MEANS	Source code
CN_PRIOR_MEANS	Source code
CN_PRIOR_SDS	Source code
CN_SDS	Source code
CopyNumScanParams	Man page Source code
CopyNumScanParams-class	Man page
EMupdates	Man page
EMupdates,EmissionParam-method	Man page
EMupdates,HmmParam-method	Man page
EmissionParam	Man page
EmissionParam,missing-method	Man page
EmissionParam,numeric-method	Man page
EmissionView	Source code
FV_columns	Source code
FilterParam	Man page Source code
FilterParam-class	Man page
HMM	Man page Source code
HMM-class	Man page
HMMList	Man page Source code
HMMList-class	Man page
HMM_STATES	Source code
HmmParam	Man page
HmmParam,matrix-method	Man page
HmmParam,missing-method	Man page
HmmTrellisParam	Man page Source code
IdiogramParams	Man page Source code
IdiogramParams-class	Man page
LogLik	Man page Source code
LogLik-class	Man page
NA_Rle	Source code
NA_filter	Man page
NA_filter,SnpArrayExperiment-method	Man page
NA_filter,character-method	Man page
NA_filter,list-method	Man page
NA_filter,numeric-method	Man page
NA_filter,oligoSnpSet-method	Man page
SnpArrayExperiment	Man page
SnpArrayExperiment,matrix-method	Man page
SnpArrayExperiment,missing-method	Man page
SnpArrayExperiment-class	Man page
SnpExperiment	Man page
SnpExperiment,ArrayViews-method	Man page
SnpGRanges	Man page
SnpGRanges,GRanges-method	Man page
SnpGRanges,missing-method	Man page
SnpGRanges-class	Man page
TransitionParam	Man page
TransitionParam,missing-method	Man page
TransitionParam,numeric-method	Man page
VanillaICE	Man page
[,ArrayViews,ANY,ANY,ANY-method	Man page
acf2	Man page Source code
assayList	Source code
assayNames	Source code
autosomes	Source code
baf,ArrayViews-method	Man page
baf,SnpArrayExperiment-method	Man page
bafFile	Man page
bafFile,ArrayViews-method	Man page
baf_means	Man page
baf_means,ArrayViews-method	Man page
baf_means,EmissionParam-method	Man page
baf_means,HmmParam-method	Man page
baf_means<-	Man page
baf_means<-,EmissionParam,numeric-method	Man page
baf_sds	Man page
baf_sds,EmissionParam-method	Man page
baf_sds,HmmParam-method	Man page
baf_sds<-	Man page
baf_sds<-,EmissionParam,numeric-method	Man page
bafvar	Source code
baumWelchUpdate	Man page Source code
calculateEmission	Man page
calculateEmission,RangedSummarizedExperiment-method	Man page
calculateEmission,list-method	Man page
calculateEmission,numeric-method	Man page
calculateViterbi	Source code
chromosomeRunLengths	Source code
cn_alleles	Source code
cn_means	Man page
cn_means,EmissionParam-method	Man page
cn_means,HmmParam-method	Man page
cn_means<-	Man page
cn_means<-,EmissionParam,numeric-method	Man page
cn_sds	Man page
cn_sds,EmissionParam-method	Man page
cn_sds,HmmParam-method	Man page
cn_sds<-	Man page
cn_sds<-,EmissionParam,numeric-method	Man page
cnvFilter	Man page
cnvFilter,GRanges-method	Man page
cnvFilter,HMM-method	Man page
cnvFilter,HMMList-method	Man page
cnvSegs	Man page
cnvSegs,HMM-method	Man page
cnvSegs,HMMList-method	Man page
cnvSegs,HmmGRanges-method	Man page
cnvar	Source code
colModes	Man page Source code
colnames	Man page
colnames,ArrayViews-method	Man page
colnames<-	Man page
colnames<-,ArrayViews,character-method	Man page
computeHeterozygosity	Source code
copyNumber,SnpArrayExperiment-method	Man page
deletion	Man page
deletion,HMM-method	Man page
dim,ArrayViews-method	Man page
doUpdate	Man page Source code
dropDuplicatedMapLocs	Man page Source code
dropSexChrom	Man page Source code
dtrnorm	Source code
duplication	Man page
duplication,HMM-method	Man page
duplication,HMMList-method	Man page
emission	Man page
emission,HmmParam-method	Man page
emission<-	Man page
emission<-,HMM-method	Man page
emission<-,HmmParam-method	Man page
emissionParam	Man page
emissionParam,HMM-method	Man page
emissionParam,HmmGRanges-method	Man page
emissionParam,HmmParam-method	Man page
emissionParam<-	Man page
emissionParam<-,HmmGRanges,EmissionParam-method	Man page
emissionParam<-,HmmParam,EmissionParam-method	Man page
expandCnTwo	Source code
expandFun	Source code
filter2	Source code
filters	Man page
filters,HMM-method	Man page
filters,HmmParam-method	Man page
flagHemDelWithHets	Source code
flagHomDelWithHets	Source code
genotypes	Man page
genotypes,ArrayViews-method	Man page
genotypes,SnpArrayExperiment-method	Man page
getCrlmmReference	Source code
getCytoband	Source code
getExampleSnpExperiment	Man page Source code
getHmmParams	Man page
getHmmParams,HMM-method	Man page
getHmmParams,HmmParam-method	Man page
getVarInEnv	Source code
grangesData	Source code
gtFile	Man page
gtFile,ArrayViews-method	Man page
gtvar	Source code
hemizygous	Man page
hemizygous,HMM-method	Man page
hemizygous,HMMList-method	Man page
hmm2	Man page
hmm2,ArrayViews-method	Man page
hmm2,SnpArrayExperiment-method	Man page
hmm2,oligoSnpSet-method	Man page
hmmFile	Source code
hmmResults	Man page
homozygous	Man page
homozygous,HMM-method	Man page
homozygous,HMMList-method	Man page
isCnAssays	Source code
isHeterozygous	Man page
isHeterozygous,ArrayViews-method	Man page
isHeterozygous,SnpArrayExperiment-method	Man page
isHeterozygous,matrix-method	Man page
isHeterozygous,numeric-method	Man page
isLoaded	Source code
isNonDecreasing	Source code
length,LogLik-method	Man page
loader	Source code
lowlevelFiles	Source code
lrr,ArrayViews-method	Man page
lrr,SnpArrayExperiment-method	Man page
lrrFile	Man page
lrrFile,ArrayViews-method	Man page
lrrFile<-	Man page
lrrFile<-,ArrayViews-method	Man page
matrixOrNULL	Man page
matrixOrNULL-class	Man page
modelHomozygousRegions	Source code
ncol,ArrayViews-method	Man page
ncol,HmmParam-method	Man page
nrow,ArrayViews-method	Man page
nrow,HmmParam-method	Man page
numberFeatures	Man page
numberFeatures,FilterParam-method	Man page
numberFeatures,HMM-method	Man page
numberFeatures,HmmGRanges-method	Man page
numberStates	Source code
panelIdiogram	Source code
parseSourceFile	Man page
parseSourceFile,ArrayViews,CopyNumScanParams-method	Man page
parsedPath	Man page
parsedPath,ArrayViews-method	Man page
paste1	Source code
plot,IdiogramParams,ANY-method	Man page
plot,IdiogramParams-method	Man page
plotIdiogram	Source code
posteriorProb	Source code
prC1	Source code
prC2	Source code
prC3	Source code
prC4	Source code
probability	Man page
probability,FilterParam-method	Man page
readAssays	Source code
reduceCnTwo	Source code
requiredAssays	Source code
rescale	Man page Source code
rowMAD	Man page Source code
rowModes	Man page Source code
rtrnorm	Source code
runningAvg	Source code
sapply,ArrayViews-method	Man page
scalars	Source code
scaleForwardBackward	Source code
segs	Man page
segs,HMM-method	Man page
segs,HMMList-method	Man page
show,ArrayViews-method	Man page
show,CopyNumScanParams-method	Man page
show,EmissionParam-method	Man page
show,FilterParam-method	Man page
show,HMM-method	Man page
show,HMMList-method	Man page
show,HmmParam-method	Man page
show,IdiogramParams-method	Man page
show,LogLik-method	Man page
show,TransitionParam-method	Man page
show,Viterbi-method	Man page
shrink	Source code
shrinkBafParam	Source code
snpArrayAssays	Man page Source code
snp_exp	Man page
sourcePaths	Man page
sourcePaths,ArrayViews-method	Man page
start,ArrayViews-method	Man page
start,oligoSnpSet-method	Man page
state,FilterParam-method	Man page
state,HMM-method	Man page
state,HmmGRanges-method	Man page
state,Viterbi-method	Man page
state-methods	Man page
sweepMode	Man page
sweepMode,SnpArrayExperiment-method	Man page
threshold	Man page Source code
trnorm	Source code
unlist,HMMList-method	Man page
updateBafParam	Source code
updateCnParam	Source code
updateHmmParams	Man page Source code
updateLogLik	Source code
updateParam	Source code
viewports	Man page Source code
writeHmm	Source code
xygrid	Man page Source code
xyplotList	Man page
xyplotList,GRangesList,SnpArrayExperiment-method	Man page
xyplotList,HmmGRanges,SnpArrayExperiment-method	Man page
yLimits	Source code