A Hidden Markov Model for high throughput genotyping arrays

Documentation for package ‘VanillaICE’ version 1.64.1

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

-- 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
copyNumber-method	Accessor for SNP genotypes
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-class	Container for the segmented data and the 6-state HMM model parameters
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
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 --

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
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

-- 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