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VanillaICE (version 1.34.0)

A Hidden Markov Model for high throughput genotyping arrays

Description

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

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Version

Version

1.34.0

License

LGPL-2

Maintainer

Robert Scharpf

Last Published

February 15th, 2017

Functions in VanillaICE (1.34.0)

HmmOptionList-class

Defunct functions/classes/methods in the VanillaICE package
CopyNumScanParams-class

Parameters for parsing source files containing SNP-array processed data, such as GenomeStudio files for the Illumina platform
IdiogramParams

Constructor for IdiogramParam objects
SnpExperiment

Constructor for SnpArrayExperiment
SnpArrayExperiment-class

A RangedSummarizedExperiment-derived class of marker-level SNP array data for copy number inference
icePlatforms

List platforms for which ICE option is supported.
cnvFilter

Filter the HMM-derived genomic ranges for copy number variants
IdiogramParams-class

Paramater class for plotting idiograms
start,oligoSnpSet-method

Retrieve genomic location of SNPs
doUpdate

Helper function to determine whether to update the HMM parameters via the Baum-Welch algorithm
state-methods

Accessor for the Viterbi state path
TransitionParam

Constructor for TransitionParam class
HMMList-class

Class, constructor, and methods for representing HMM results from multiple samples
numberFeatures

The number of SNP/nonpolymorphic probes contained in a genomic interval
lrrFile

Accessors for objects of class ArrayViews
snp_exp

An example SnpArrayExperiment
HmmParam

Constructor for HmmParam class
emission

Methods to set and get emission probabilities
HmmTrellisParam

Constructor for HmmTrellisParam class
genotypes

Accessor for SNP genotypes
sweepMode

Sweep the modal log R ratio (by row or column) from a matrix of log R ratios
emissionParam

Accessor for parameters used to compute emission probabilities
segs

Accessor for the HMM segments
read.bsfiles

Deprecated function in VanillaICE
threshold

Threshold numeric values
LogLik-class

Classes and methods for storing/getting log-likelihoods from Viterbi algorithm
isHeterozygous

Assess whether genotype is heterozygous based on BAFs
dropDuplicatedMapLocs

Drop markers on the same chromosome having the same genomic coordinates
hmmResults

Example output from the hidden markov model
FilterParam-class

Container for the common criteria used to filtering genomic ranges
rescale

Rescale a numeric vector
show,Viterbi-method

Show method for objects of class Viterbi
xyplotList

Lattice-style plots for granges and SnpArrayExperiment objects
HMMList

Constructor for HMMList class
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
hmm

Deprecated functions in the VanillaICE package
HMM-class

Container for the segmented data and the 6-state HMM model parameters
BeadStudioSetList

Deprecated BeadStudioSet and BeadStudioSetList
getHmmParams

Accessor for HMM model parameters
LogLik

Constructor for LogLik class
viterbi2Wrapper

Wrapper function for fitting the viterbi algorithm
rowModes

Robust statistics for matrices
sourcePaths

Accessor for file paths containing SNP-level summaries
dropSexChrom

Filter sex chromosomes
hmm2

Fit a 6-state HMM to log R ratios and B allele frequencies estimated from SNP arrays
matrixOrNULL

A class allowing matrix or NULL objects
calculateEmission

Calculate the emission probabilities for the 6-state HMM
[[,oligoSetList,ANY,ANY-method

Subset method for deprecated oligoSetList
baumWelchUpdate

Function for updating parameters for emission probabilities
updateHmmParams

Run the Baum-Welch algorithm to update HMM parameters
state,HmmGRanges-method

Accessor for copy number state
NA_filter

Remove SNPs with NAs in any of the low-level estimates
filters

Accessor for HMM filter parameters
ArrayViews-class

ArrayViews class, constructor, and methods
probability

Accessor for probability filter
acf2

Calculate lag10 autocorrelation
parsedPath

Complete path to directory for keeping parsed files
constrainMu2

Constraints for updating the means of the copy number states
SnpGRanges-class

An extension to GRanges for representing SNPs
getExampleSnpExperiment

Create an example SnpArrayExperiment from source files containing marker-level genomic data that are provided in this package
parseSourceFile

Function for parsing GenomeStudio files
cn_means

A parameter class for computing Emission probabilities
snpArrayAssays

Create an assays object from log R ratios and B allele frequencies