API for rscharpf/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
ArrayViews Man page
ArrayViews,numeric,numeric-method Man page
ArrayViews-class Man page
CopyNumScanParams Man page
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
FilterParam Man page
FilterParam-class Man page
HMM Man page
HMM-class Man page
HMMList Man page
HMMList-class Man page
HmmParam Man page
HmmParam,matrix-method Man page
HmmParam,missing-method Man page
HmmTrellisParam Man page
IdiogramParams Man page
IdiogramParams-class Man page
LogLik Man page
LogLik-class Man page
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
VanillaICE-package Man page
[,ArrayViews,ANY,ANY,ANY-method Man page
acf2 Man page
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
baumWelchUpdate Man page
calculateEmission Man page
calculateEmission,RangedSummarizedExperiment-method Man page
calculateEmission,list-method Man page
calculateEmission,numeric-method Man page
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
colModes Man page
colnames Man page
colnames,ArrayViews-method Man page
colnames<- Man page
colnames<-,ArrayViews,character-method Man page
copyNumber,SnpArrayExperiment-method Man page
deletion Man page
deletion,HMM-method Man page
dim,ArrayViews-method Man page
doUpdate Man page
dropDuplicatedMapLocs Man page
dropSexChrom Man page
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
filters Man page
filters,HMM-method Man page
filters,HmmParam-method Man page
genotypes Man page
genotypes,ArrayViews-method Man page
genotypes,SnpArrayExperiment-method Man page
getExampleSnpExperiment Man page
getHmmParams Man page
getHmmParams,HMM-method Man page
getHmmParams,HmmParam-method Man page
gtFile Man page
gtFile,ArrayViews-method Man page
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
hmmResults Man page
homozygous Man page
homozygous,HMM-method Man page
homozygous,HMMList-method Man page
isHeterozygous Man page
isHeterozygous,ArrayViews-method Man page
isHeterozygous,SnpArrayExperiment-method Man page
isHeterozygous,matrix-method Man page
isHeterozygous,numeric-method Man page
length,LogLik-method Man page
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
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
parseSourceFile Man page
parseSourceFile,ArrayViews,CopyNumScanParams-method Man page
parsedPath Man page
parsedPath,ArrayViews-method Man page
plot,IdiogramParams,ANY-method Man page
plot,IdiogramParams-method Man page
probability Man page
probability,FilterParam-method Man page
rescale Man page
rowMAD Man page
rowModes Man page
sapply,ArrayViews-method Man page
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
snpArrayAssays Man page
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
unlist,HMMList-method Man page
updateHmmParams Man page
viewports Man page
xygrid Man page
xyplotList Man page
xyplotList,GRangesList,SnpArrayExperiment-method Man page
xyplotList,HmmGRanges,SnpArrayExperiment-method Man page
rscharpf/VanillaICE documentation built on May 15, 2019, 5:51 p.m.