VanillaICE: A Hidden Markov Model for high throughput genotyping arrays
Version 1.38.0

Hidden Markov Models for characterizing chromosomal alterations in high throughput SNP arrays.

AuthorRobert Scharpf <rscharpf@jhu.edu>, Kevin Scharpf, and Ingo Ruczinski <ingo@jhsph.edu>
Bioconductor views CopyNumberVariation
Date of publicationNone
MaintainerRobert Scharpf <rscharpf@jhsph.edu>
LicenseLGPL-2
Version1.38.0
Package repositoryView on Bioconductor
InstallationInstall the latest version of this package by entering the following in R:
source("https://bioconductor.org/biocLite.R")
biocLite("VanillaICE")

Popular man pages

acf2: Calculate lag10 autocorrelation
dropSexChrom: Filter sex chromosomes
isHeterozygous: Assess whether genotype is heterozygous based on BAFs
LogLik: Constructor for LogLik class
parseSourceFile: Function for parsing GenomeStudio files
probability: Accessor for probability filter
SnpGRanges: An extension to GRanges for representing SNPs
See all...

All man pages Function index File listing

Man pages

acf2: Calculate lag10 autocorrelation
ArrayViews-class: ArrayViews class, constructor, and methods
baumWelchUpdate: Function for updating parameters for emission probabilities
calculateEmission: Calculate the emission probabilities for the 6-state HMM
cnvFilter: Filter the HMM-derived genomic ranges for copy number...
CopyNumScanParams: Parameters for parsing source files containing SNP-array...
doUpdate: Helper function to determine whether to update the HMM...
dropDuplicatedMapLocs: Drop markers on the same chromosome having the same genomic...
dropSexChrom: Filter sex chromosomes
emission: Methods to set and get emission probabilities
emissionParam: Accessor for parameters used to compute emission...
EmissionParam-methods: A parameter class for computing Emission probabilities
FilterParam-class: Container for the common criteria used to filtering genomic...
filters: Accessor for HMM filter parameters
getExampleSnpExperiment: Create an example SnpArrayExperiment from source files...
getHmmParams: Accessor for HMM model parameters
HMM: Container for the segmented data and the 6-state HMM model...
hmm2: Fit a 6-state HMM to log R ratios and B allele frequencies...
HmmGRanges-methods: Accessor for copy number state
HMMList: Constructor for 'HMMList' class
HMMList-class: Class, constructor, and methods for representing HMM results...
HmmParam: Constructor for HmmParam class
hmmResults: Example output from the hidden markov model
HmmTrellisParam: Constructor for HmmTrellisParam class
IdiogramParam-class: Constructor for IdiogramParam objects
IdiogramParams-class: Paramater class for plotting idiograms
IO: Accessors for objects of class ArrayViews
isHeterozygous: Assess whether genotype is heterozygous based on BAFs
LogLik: Constructor for LogLik class
LogLik-class: Classes and methods for storing/getting log-likelihoods from...
LowLevelSummaries: Accessor for SNP genotypes
matrixOrNULL-class: A class allowing matrix or NULL objects
NA_filter: Remove SNPs with NAs in any of the low-level estimates
numberFeatures: The number of SNP/nonpolymorphic probes contained in a...
parsedPath: Complete path to directory for keeping parsed files
parseSourceFile: Function for parsing GenomeStudio files
plotting: Lattice-style plots for granges and SnpArrayExperiment...
probability: Accessor for probability filter
rescale: Rescale a numeric vector
robust-statistics: Robust statistics for matrices
segs: Accessor for the HMM segments
snpArrayAssays: Create an assays object from log R ratios and B allele...
SnpArrayExperiment-class: A RangedSummarizedExperiment-derived class of marker-level...
snp_exp: An example SnpArrayExperiment
SnpExperiment: Constructor for SnpArrayExperiment
SnpGRanges: An extension to GRanges for representing SNPs
sourcePaths: Accessor for file paths containing SNP-level summaries
start-oligoSnpSet-method: Retrieve genomic location of SNPs
state-methods: Accessor for the Viterbi state path
sweepMode: Sweep the modal log R ratio (by row or column) from a matrix...
threshold: Threshold numeric values
TransitionParam: Constructor for TransitionParam class
updateHmmParams: Run the Baum-Welch algorithm to update HMM parameters
VanillaICE: A hidden markov model for detection of germline copy number...
viewports: Default viewports for plotting CNV data with lattice-style...
Viterbi-methods: Show method for objects of class 'Viterbi'

Functions

"[",ArrayViews,ANY-method Man page
$,ArrayViews-method Man page
$<-,ArrayViews-method Man page
'[',ArrayViews,ANY-method Man page
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
ShallowSimpleListAssays Source code
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 Source code
apply_cnv_filters 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
calculateBAFEmission Source code
calculateEmission Man page Source code
calculateEmission,RangedSummarizedExperiment-method Man page
calculateEmission,list-method Man page
calculateEmission,numeric-method Man page
calculateTransitionProbs Source code
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 Source code
colnames,ArrayViews-method Man page
colnames<- Man page
colnames<-,ArrayViews,character-method Man page
computeHeterozygosity Source code
copyNumber,SnpArrayExperiment-method Man page
cytobandColors Source code
deletion Man page
deletion,HMM-method Man page
dim,ArrayViews-method Man page
doUpdate Man page Source code
drawPolygon Source code
drawStalk 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
find_xlim_percent Source code
firstSegment Source code
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
hmm Source code
hmm2 Man page
hmm2,ArrayViews-method Man page
hmm2,SnpArrayExperiment-method Man page
hmm2,oligoSnpSet-method Man page
hmmFile Source code
hmmResults Man page
hmm_states Source code
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
lapply 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
onAttach Source code
onUnload Source code
panelIdiogram Source code
parseSourceFile Man page Source code
parseSourceFile,ArrayViews,CopyNumScanParams-method Man page
parsedPath Man page
parsedPath,ArrayViews-method Man page
paste1 Source code
path 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
resolveIndex Source code
rowMAD Man page Source code
rowModes Man page Source code
rownames 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
snp_id_column Source code
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
update_baf 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
xyplotlist Source code
yLimits Source code

Files

CHANGES
DESCRIPTION
NAMESPACE
NEWS
R
R/AllClasses.R
R/AllGenerics.R
R/datasets.R
R/functions.R
R/help.R
R/hmm-methods.R
R/methods-ArrayViews.R
R/methods-CopyNumScanParams.R
R/methods-EmissionParam.R
R/methods-FilterParam.R
R/methods-HMM.R
R/methods-HMMList.R
R/methods-HmmGRanges.R
R/methods-HmmParam.R
R/methods-HmmTrellisParam.R
R/methods-IdiogramParams.R
R/methods-LogLik.R
R/methods-SnpArrayExperiment.R
R/methods-SnpDataFrame.R
R/methods-TransitionParam.R
R/methods-Viterbi.R
R/updates.R
R/zzz.R
build
build/vignette.rds
changelog
data
data/snp_exp.rda
inst
inst/CITATION
inst/NEWS.Rd
inst/doc
inst/doc/VanillaICE.R
inst/doc/VanillaICE.Rnw
inst/doc/VanillaICE.pdf
inst/doc/crlmmDownstream.R
inst/doc/crlmmDownstream.Rnw
inst/doc/crlmmDownstream.pdf
inst/extdata
inst/extdata/FinalReport1664.txt
inst/extdata/FinalReport1675.txt
inst/extdata/FinalReport1686.txt
inst/extdata/FinalReport6841.txt
inst/extdata/FinalReport6872.txt
inst/extdata/FinalReport6903.txt
inst/extdata/SNP_info.csv
inst/extdata/sample_data.csv
inst/extdata/snp_exp.rda
inst/illumina
inst/illumina/illuminaEx.txt
inst/scripts
inst/scripts/crlmmDownstream.Rnw
inst/scripts/crlmmDownstream.pdf
inst/scripts/runcrlmm.R
inst/test
inst/test/crlmmDownstream.Rnw
inst/testing
inst/unitTests
inst/unitTests/Makefile
inst/unitTests/TestData.R
inst/unitTests/test_ArrayViews.R
inst/unitTests/test_BeadStudioSet.R
inst/unitTests/test_FilterParam.R
inst/unitTests/test_HmmGRanges.R
inst/unitTests/test_HmmParam.R
inst/unitTests/test_SnpArrayExperiment.R
inst/unitTests/test_SnpGRanges.R
inst/unitTests/test_SummarizedExperiment.R
inst/unitTests/test_acf2.R
inst/unitTests/test_constraints.R
inst/unitTests/test_hmm.R
inst/unitTests/test_loess.R
inst/unitTests/test_oligoSetList.R
inst/unitTests/test_rowMAD.R
inst/unitTests/test_scaleBy.R
inst/unitTests/test_sweepMode.R
inst/unitTests/test_viterbi.R
man
man/ArrayViews-class.Rd
man/CopyNumScanParams.Rd
man/EmissionParam-methods.Rd
man/FilterParam-class.Rd
man/HMM.Rd
man/HMMList-class.Rd
man/HMMList.Rd
man/HmmGRanges-methods.Rd
man/HmmParam.Rd
man/HmmTrellisParam.Rd
man/IO.Rd
man/IdiogramParam-class.Rd
man/IdiogramParams-class.Rd
man/LogLik-class.Rd
man/LogLik.Rd
man/LowLevelSummaries.Rd
man/NA_filter.Rd
man/SnpArrayExperiment-class.Rd
man/SnpExperiment.Rd
man/SnpGRanges.Rd
man/TransitionParam.Rd
man/VanillaICE.Rd
man/Viterbi-methods.Rd
man/acf2.Rd
man/baumWelchUpdate.Rd
man/calculateEmission.Rd
man/cnvFilter.Rd
man/doUpdate.Rd
man/dropDuplicatedMapLocs.Rd
man/dropSexChrom.Rd
man/emission.Rd
man/emissionParam.Rd
man/filters.Rd
man/getExampleSnpExperiment.Rd
man/getHmmParams.Rd
man/hmm2.Rd
man/hmmResults.Rd
man/isHeterozygous.Rd
man/matrixOrNULL-class.Rd
man/numberFeatures.Rd
man/parseSourceFile.Rd
man/parsedPath.Rd
man/plotting.Rd
man/probability.Rd
man/rescale.Rd
man/robust-statistics.Rd
man/segs.Rd
man/snpArrayAssays.Rd
man/snp_exp.Rd
man/sourcePaths.Rd
man/start-oligoSnpSet-method.Rd
man/state-methods.Rd
man/sweepMode.Rd
man/threshold.Rd
man/updateHmmParams.Rd
man/viewports.Rd
src
src/Makevars
src/rinit.c
src/viterbi.c
tests
tests/doRUnit.R
vignettes
vignettes/VanillaICE.Rnw
vignettes/crlmmDownstream.Rnw
vignettes/ice.bib
VanillaICE documentation built on May 20, 2017, 10:15 p.m.

Questions? Problems? Suggestions? Tweet to @rdrrHQ or email at ian@mutexlabs.com.

Please suggest features or report bugs in the GitHub issue tracker.

All documentation is copyright its authors; we didn't write any of that.