# A Hidden Markov Model for high throughput genotyping arrays

## Documentation for package ‘VanillaICE’ version 1.32.0

- DESCRIPTION file.
- User guides, package vignettes and other documentation.
- Package NEWS.

## Help Pages

A B C D E F G H I L M N P R S T U V X misc

VanillaICE-package | A hidden markov model for detection of germline copy number variants from arrays

## -- A --

acf2 | Calculate lag10 autocorrelation
ArrayViews | ArrayViews class, constructor, and methods
ArrayViews-class | ArrayViews class, constructor, and methods
ArrayViews-method | ArrayViews class, constructor, and methods

## -- B --

baf-method | Accessor for SNP genotypes
bafFile | Accessors for objects of class ArrayViews
bafFile-method | Accessors for objects of class ArrayViews
baf_means | A parameter class for computing Emission probabilities
baf_means-method | ArrayViews class, constructor, and methods
baf_means-method | A parameter class for computing Emission probabilities
baf_means<- | A parameter class for computing Emission probabilities
baf_means<--method | A parameter class for computing Emission probabilities
baf_sds | A parameter class for computing Emission probabilities
baf_sds-method | A parameter class for computing Emission probabilities
baf_sds<- | A parameter class for computing Emission probabilities
baf_sds<--method | A parameter class for computing Emission probabilities
baumWelchUpdate | Function for updating parameters for emission probabilities

## -- C --

calculateEmission | Calculate the emission probabilities for the 6-state HMM
calculateEmission-method | Calculate the emission probabilities for the 6-state HMM
cnvFilter | Filter the HMM-derived genomic ranges for copy number variants
cnvFilter-method | Filter the HMM-derived genomic ranges for copy number variants
cnvSegs | Filter the HMM-derived genomic ranges for copy number variants
cnvSegs-method | Filter the HMM-derived genomic ranges for copy number variants
cn_means | A parameter class for computing Emission probabilities
cn_means-method | A parameter class for computing Emission probabilities
cn_means<- | A parameter class for computing Emission probabilities
cn_means<--method | A parameter class for computing Emission probabilities
cn_sds | A parameter class for computing Emission probabilities
cn_sds-method | A parameter class for computing Emission probabilities
cn_sds<- | A parameter class for computing Emission probabilities
cn_sds<--method | A parameter class for computing Emission probabilities
colModes | Robust statistics for matrices
colnames | ArrayViews class, constructor, and methods
colnames-method | ArrayViews class, constructor, and methods
colnames<- | ArrayViews class, constructor, and methods
colnames<--method | ArrayViews class, constructor, and methods
constrainMu2 | Constraints for updating the means of the copy number states
constrainSd2 | Constraints for updating the means of the copy number states
copyNumber-method | Accessor for SNP genotypes
copyNumberLimits | Constraints for updating the means of the copy number states
CopyNumScanParams | Parameters for parsing source files containing SNP-array processed data, such as GenomeStudio files for the Illumina platform
CopyNumScanParams-class | Parameters for parsing source files containing SNP-array processed data, such as GenomeStudio files for the Illumina platform

## -- D --

deletion | Filter the HMM-derived genomic ranges for copy number variants
deletion-method | Filter the HMM-derived genomic ranges for copy number variants
dim-method | ArrayViews class, constructor, and methods
doUpdate | Helper function to determine whether to update the HMM parameters via the Baum-Welch algorithm
dropDuplicatedMapLocs | Drop markers on the same chromosome having the same genomic coordinates
dropSexChrom | Filter sex chromosomes
duplication | Filter the HMM-derived genomic ranges for copy number variants
duplication-method | Filter the HMM-derived genomic ranges for copy number variants

## -- E --

emission | Methods to set and get emission probabilities
emission-method | Methods to set and get emission probabilities
emission<- | Methods to set and get emission probabilities
emission<--method | Methods to set and get emission probabilities
EmissionParam | A parameter class for computing Emission probabilities
emissionParam | Accessor for parameters used to compute emission probabilities
EmissionParam-method | A parameter class for computing Emission probabilities
emissionParam-method | Accessor for parameters used to compute emission probabilities
emissionParam<- | Accessor for parameters used to compute emission probabilities
emissionParam<--method | Accessor for parameters used to compute emission probabilities
EMupdates | A parameter class for computing Emission probabilities
EMupdates-method | A parameter class for computing Emission probabilities

## -- F --

FilterParam | Container for the common criteria used to filtering genomic ranges
FilterParam-class | Container for the common criteria used to filtering genomic ranges
filters | Accessor for HMM filter parameters
filters-method | Accessor for HMM filter parameters

## -- G --

genotypes | Accessor for SNP genotypes
genotypes-method | Accessor for SNP genotypes
getExampleSnpExperiment | Create an example SnpArrayExperiment from source files containing marker-level genomic data that are provided in this package
getHmmParams | Accessor for HMM model parameters
getHmmParams-method | Accessor for HMM model parameters
gtFile | Accessors for objects of class ArrayViews
gtFile-method | Accessors for objects of class ArrayViews

## -- H --

hemizygous | Filter the HMM-derived genomic ranges for copy number variants
hemizygous-method | Filter the HMM-derived genomic ranges for copy number variants
HMM | Container for the segmented data and the 6-state HMM model parameters
hmm | Deprecated functions in the VanillaICE package
HMM-class | Container for the segmented data and the 6-state HMM model parameters
hmm-method | Deprecated functions in the VanillaICE package
hmm2 | Fit a 6-state HMM to log R ratios and B allele frequencies estimated from SNP arrays
hmm2-method | Fit a 6-state HMM to log R ratios and B allele frequencies estimated from SNP arrays
HmmGRanges | ##HmmGRanges container ##
HMMList | Constructor for 'HMMList' class
HMMList-class | Class, constructor, and methods for representing HMM results from multiple samples
HmmParam | Constructor for HmmParam class
HmmParam-method | Constructor for HmmParam class
hmmResults | Example output from the hidden markov model
HmmTrellisParam | Constructor for HmmTrellisParam class
homozygous | Filter the HMM-derived genomic ranges for copy number variants
homozygous-method | Filter the HMM-derived genomic ranges for copy number variants

## -- I --

icePlatforms | List platforms for which ICE option is supported.
IdiogramParams | Constructor for IdiogramParam objects
IdiogramParams-class | Paramater class for plotting idiograms
isHeterozygous | Assess whether genotype is heterozygous based on BAFs
isHeterozygous-method | Assess whether genotype is heterozygous based on BAFs

## -- L --

length-method | Classes and methods for storing/getting log-likelihoods from Viterbi algorithm
LogLik | Constructor for LogLik class
LogLik-class | Classes and methods for storing/getting log-likelihoods from Viterbi algorithm
lrr-method | Accessor for SNP genotypes
lrrFile | Accessors for objects of class ArrayViews
lrrFile-method | Accessors for objects of class ArrayViews
lrrFile<- | Accessors for objects of class ArrayViews
lrrFile<--method | Accessors for objects of class ArrayViews

## -- M --

matrixOrNULL | A class allowing matrix or NULL objects
matrixOrNULL-class | A class allowing matrix or NULL objects

## -- N --

NA_filter | Remove SNPs with NAs in any of the low-level estimates
NA_filter-method | Remove SNPs with NAs in any of the low-level estimates
ncol-method | ArrayViews class, constructor, and methods
ncol-method | Constructor for HmmParam class
nrow-method | ArrayViews class, constructor, and methods
nrow-method | Constructor for HmmParam class
numberFeatures | The number of SNP/nonpolymorphic probes contained in a genomic interval
numberFeatures-method | The number of SNP/nonpolymorphic probes contained in a genomic interval

## -- P --

parsedPath | Complete path to directory for keeping parsed files
parsedPath-method | Complete path to directory for keeping parsed files
parseSourceFile | Function for parsing GenomeStudio files
parseSourceFile-method | Function for parsing GenomeStudio files
plot-method | Constructor for IdiogramParam objects
probability | Accessor for probability filter
probability-method | Container for the common criteria used to filtering genomic ranges

## -- R --

rescale | Rescale a numeric vector
robustSds | Deprecated functions in the VanillaICE package
rowMAD | Robust statistics for matrices
rowModes | Robust statistics for matrices

## -- S --

sapply-method | ArrayViews class, constructor, and methods
segs | Accessor for the HMM segments
segs-method | Filter the HMM-derived genomic ranges for copy number variants
segs-method | Accessor for the HMM segments
show-method | ArrayViews class, constructor, and methods
show-method | Parameters for parsing source files containing SNP-array processed data, such as GenomeStudio files for the Illumina platform
show-method | A parameter class for computing Emission probabilities
show-method | Container for the common criteria used to filtering genomic ranges
show-method | Container for the segmented data and the 6-state HMM model parameters
show-method | Class, constructor, and methods for representing HMM results from multiple samples
show-method | Constructor for HmmParam class
show-method | Paramater class for plotting idiograms
show-method | Classes and methods for storing/getting log-likelihoods from Viterbi algorithm
show-method | Constructor for TransitionParam class
show-method | Show method for objects of class 'Viterbi'
snpArrayAssays | Create an assays object from log R ratios and B allele frequencies
SnpArrayExperiment | A RangedSummarizedExperiment-derived class of marker-level SNP array data for copy number inference
SnpArrayExperiment-class | A RangedSummarizedExperiment-derived class of marker-level SNP array data for copy number inference
SnpArrayExperiment-method | A RangedSummarizedExperiment-derived class of marker-level SNP array data for copy number inference
SnpExperiment | Constructor for SnpArrayExperiment
SnpExperiment-method | Constructor for SnpArrayExperiment
SnpGRanges | An extension to GRanges for representing SNPs
SnpGRanges-class | An extension to GRanges for representing SNPs
SnpGRanges-method | An extension to GRanges for representing SNPs
snp_exp | An example SnpArrayExperiment
sourcePaths | Accessor for file paths containing SNP-level summaries
sourcePaths-method | Accessor for file paths containing SNP-level summaries
start-method | ArrayViews class, constructor, and methods
start-method | Retrieve genomic location of SNPs
state-method | Container for the common criteria used to filtering genomic ranges
state-method | Container for the segmented data and the 6-state HMM model parameters
state-method | Accessor for copy number state
state-method | Accessor for the Viterbi state path
state-methods | Accessor for the Viterbi state path
sweepMode | Sweep the modal log R ratio (by row or column) from a matrix of log R ratios
sweepMode-method | Sweep the modal log R ratio (by row or column) from a matrix of log R ratios

## -- T --

threshold | Threshold numeric values
TransitionParam | Constructor for TransitionParam class
TransitionParam-method | Constructor for TransitionParam class

## -- U --

unlist-method | Class, constructor, and methods for representing HMM results from multiple samples
updateHmmParams | Run the Baum-Welch algorithm to update HMM parameters

## -- V --

VanillaICE | A hidden markov model for detection of germline copy number variants from arrays
viewports | Default viewports for plotting CNV data with lattice-style graphics
viterbi2Wrapper | Wrapper function for fitting the viterbi algorithm

## -- X --

xygrid | Lattice-style plots for granges and SnpArrayExperiment objects
xyplotList | Lattice-style plots for granges and SnpArrayExperiment objects
xyplotList-method | Lattice-style plots for granges and SnpArrayExperiment objects

## -- misc --

"["-method | ArrayViews class, constructor, and methods
$-method | ArrayViews class, constructor, and methods
$<--method | ArrayViews class, constructor, and methods
'['-method | ArrayViews class, constructor, and methods
[-method | ArrayViews class, constructor, and methods
[[-method | Subset method for deprecated 'oligoSetList'