Package: VanillaICE 1.67.0

Robert Scharpf

VanillaICE: A Hidden Markov Model for high throughput genotyping arrays

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

Authors:Robert Scharpf [aut, cre]

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NEWS

# Install 'VanillaICE' in R:

install.packages('VanillaICE', repos = c('https://bioc.r-universe.dev', 'https://cloud.r-project.org'))

Datasets:

snp_exp - An example SnpArrayExperiment

On BioConductor:VanillaICE-1.67.0(bioc 3.20)VanillaICE-1.66.0(bioc 3.19)

This package does not link to any Github/Gitlab/R-forge repository. No issue tracker or development information is available.

bioconductor-package

79 exports 1.24 score 85 dependencies 1 dependents 3 mentions

Last updated 2 months agofrom:76138760cb

Exports:acf2 ArrayViews baf baf_means baf_means<-baf_sds baf_sds<-bafFile baumWelchUpdate calculateEmission cn_means cn_means<-cn_sds cn_sds<-cnvFilter cnvSegs colModes colnames colnames<-copyNumber CopyNumScanParams deletion doUpdate dropDuplicatedMapLocs dropSexChrom duplication emission emission<-emissionParam EmissionParam emissionParam<-EMupdates FilterParam filters genotypes getExampleSnpExperiment getHmmParams gtFile hemizygous HMM hmm2 HMMList HmmParam HmmTrellisParam homozygous IdiogramParams isHeterozygous LogLik lrr lrrFile lrrFile<-NA_filter ncol nrow numberFeatures parsedPath parseSourceFile plot probability rescale rowMAD rowModes sapply segs show snpArrayAssays SnpArrayExperiment SnpExperiment SnpGRanges sourcePaths start state sweepMode threshold TransitionParam updateHmmParams viewports xygrid xyplotList

Dependencies:abind affyio askpass base64 beanplot BH Biobase BiocGenerics BiocIO BiocManager BiocParallel Biostrings bit bit64 bitops blob BSgenome BSgenome.Hsapiens.UCSC.hg18 cachem cli codetools cpp11 crayon crlmm curl data.table DBI DelayedArray ellipse fastmap ff foreach formatR futile.logger futile.options GenomeInfoDb GenomeInfoDbData GenomicAlignments GenomicRanges glue httr illuminaio IRanges iterators jsonlite lambda.r lattice lifecycle limma Matrix MatrixGenerics matrixStats memoise mime mvtnorm oligoClasses openssl pkgconfig plogr preprocessCore R6 Rcpp RcppEigen RCurl restfulr Rhtslib rjson rlang Rsamtools RSQLite rtracklayer S4Arrays S4Vectors snow SparseArray statmod SummarizedExperiment sys UCSC.utils vctrs VGAM XML XVector yaml zlibbioc

crlmmDownstream

Rendered fromcrlmmDownstream.Rnwusingutils::Sweaveon Jun 30 2024.

Last update: 2020-12-08
Started: 2012-01-03

VanillaICE Vignette

Rendered fromVanillaICE.Rnwusingutils::Sweaveon Jun 30 2024.

Last update: 2020-03-16
Started: 2012-01-03

Citation

Development and contributors

Readme and manuals

Help Manual

Help page	Topics
Calculate lag10 autocorrelation	acf2
ArrayViews class, constructor, and methods	"[",ArrayViews,ANY-method $,ArrayViews-method $<-,ArrayViews-method '[',ArrayViews,ANY-method ArrayViews ArrayViews,numeric,numeric-method ArrayViews-class baf_means,ArrayViews-method colnames colnames,ArrayViews-method colnames<- colnames<-,ArrayViews,character-method dim,ArrayViews-method ncol,ArrayViews-method nrow,ArrayViews-method sapply,ArrayViews-method show,ArrayViews-method start,ArrayViews-method [,ArrayViews,ANY,ANY,ANY-method
Function for updating parameters for emission probabilities	baumWelchUpdate
Calculate the emission probabilities for the 6-state HMM	calculateEmission calculateEmission,list-method calculateEmission,numeric-method calculateEmission,RangedSummarizedExperiment-method
A parameter class for computing Emission probabilities	baf_means baf_means,EmissionParam-method baf_means,HmmParam-method baf_means<- baf_means<-,EmissionParam,numeric-method baf_sds baf_sds,EmissionParam-method baf_sds,HmmParam-method baf_sds<- baf_sds<-,EmissionParam,numeric-method cn_means cn_means,EmissionParam-method cn_means,HmmParam-method cn_means<- cn_means<-,EmissionParam,numeric-method cn_sds cn_sds,EmissionParam-method cn_sds,HmmParam-method cn_sds<- cn_sds<-,EmissionParam,numeric-method EmissionParam EmissionParam,missing-method EmissionParam,numeric-method EMupdates EMupdates,EmissionParam-method EMupdates,HmmParam-method show,EmissionParam-method
Filter the HMM-derived genomic ranges for copy number variants	cnvFilter cnvFilter,GRanges-method cnvFilter,HMM-method cnvFilter,HMMList-method cnvSegs cnvSegs,HMM-method cnvSegs,HmmGRanges-method cnvSegs,HMMList-method deletion deletion,HMM-method duplication duplication,HMM-method duplication,HMMList-method hemizygous hemizygous,HMM-method hemizygous,HMMList-method homozygous homozygous,HMM-method homozygous,HMMList-method segs,HMMList-method
Parameters for parsing source files containing SNP-array processed data, such as GenomeStudio files for the Illumina platform	CopyNumScanParams CopyNumScanParams-class show,CopyNumScanParams-method
Helper function to determine whether to update the HMM parameters via the Baum-Welch algorithm	doUpdate
Drop markers on the same chromosome having the same genomic coordinates	dropDuplicatedMapLocs
Filter sex chromosomes	dropSexChrom
Methods to set and get emission probabilities	emission emission,HmmParam-method emission<- emission<-,HMM-method emission<-,HmmParam-method
Accessor for parameters used to compute emission probabilities	emissionParam emissionParam,HMM-method emissionParam,HmmGRanges-method emissionParam,HmmParam-method emissionParam<- emissionParam<-,HmmGRanges,EmissionParam-method emissionParam<-,HmmParam,EmissionParam-method
Container for the common criteria used to filtering genomic ranges	FilterParam FilterParam-class probability,FilterParam-method show,FilterParam-method state,FilterParam-method
Accessor for HMM filter parameters	filters filters,HMM-method filters,HmmParam-method
Accessor for SNP genotypes	baf,ArrayViews-method baf,SnpArrayExperiment-method copyNumber,SnpArrayExperiment-method genotypes genotypes,ArrayViews-method genotypes,SnpArrayExperiment-method lrr,ArrayViews-method lrr,SnpArrayExperiment-method
Create an example SnpArrayExperiment from source files containing marker-level genomic data that are provided in this package	getExampleSnpExperiment
Accessor for HMM model parameters	getHmmParams getHmmParams,HMM-method getHmmParams,HmmParam-method
Container for the segmented data and the 6-state HMM model parameters	HMM HMM-class show,HMM-method state,HMM-method
Fit a 6-state HMM to log R ratios and B allele frequencies estimated from SNP arrays	hmm2 hmm2,ArrayViews-method hmm2,oligoSnpSet-method hmm2,SnpArrayExperiment-method
Constructor for 'HMMList' class	HMMList
Class, constructor, and methods for representing HMM results from multiple samples	HMMList-class show,HMMList-method unlist,HMMList-method
Constructor for HmmParam class	HmmParam HmmParam,matrix-method HmmParam,missing-method ncol,HmmParam-method nrow,HmmParam-method show,HmmParam-method
Example output from the hidden markov model	hmmResults
Constructor for HmmTrellisParam class	HmmTrellisParam
Constructor for IdiogramParam objects	IdiogramParams plot,IdiogramParams,ANY-method plot,IdiogramParams-method
Paramater class for plotting idiograms	IdiogramParams-class show,IdiogramParams-method
Assess whether genotype is heterozygous based on BAFs	isHeterozygous isHeterozygous,ArrayViews-method isHeterozygous,matrix-method isHeterozygous,numeric-method isHeterozygous,SnpArrayExperiment-method
Constructor for LogLik class	LogLik
Classes and methods for storing/getting log-likelihoods from Viterbi algorithm	length,LogLik-method LogLik-class show,LogLik-method
Accessors for objects of class ArrayViews	bafFile bafFile,ArrayViews-method gtFile gtFile,ArrayViews-method lrrFile lrrFile,ArrayViews-method lrrFile<- lrrFile<-,ArrayViews-method
A class allowing matrix or NULL objects	matrixOrNULL matrixOrNULL-class
Remove SNPs with NAs in any of the low-level estimates	NA_filter NA_filter,character-method NA_filter,list-method NA_filter,numeric-method NA_filter,oligoSnpSet-method NA_filter,SnpArrayExperiment-method
The number of SNP/nonpolymorphic probes contained in a genomic interval	numberFeatures numberFeatures,FilterParam-method numberFeatures,HMM-method numberFeatures,HmmGRanges-method
Complete path to directory for keeping parsed files	parsedPath parsedPath,ArrayViews-method
Function for parsing GenomeStudio files	parseSourceFile parseSourceFile,ArrayViews,CopyNumScanParams-method
Accessor for probability filter	probability
Rescale a numeric vector	rescale
Robust statistics for matrices	colModes rowMAD rowModes
Accessor for the HMM segments	segs segs,HMM-method
Show method for objects of class 'Viterbi'	show,Viterbi-method
An example SnpArrayExperiment	snp_exp
Create an assays object from log R ratios and B allele frequencies	snpArrayAssays
A RangedSummarizedExperiment-derived class of marker-level SNP array data for copy number inference	SnpArrayExperiment SnpArrayExperiment,matrix-method SnpArrayExperiment,missing-method SnpArrayExperiment-class
Constructor for SnpArrayExperiment	SnpExperiment SnpExperiment,ArrayViews-method
An extension to GRanges for representing SNPs	SnpGRanges SnpGRanges,GRanges-method SnpGRanges,missing-method SnpGRanges-class
Accessor for file paths containing SNP-level summaries	sourcePaths sourcePaths,ArrayViews-method
Retrieve genomic location of SNPs	start,oligoSnpSet-method
Accessor for the Viterbi state path	state,Viterbi-method state-methods
Accessor for copy number state	state,HmmGRanges-method
Sweep the modal log R ratio (by row or column) from a matrix of log R ratios	sweepMode sweepMode,SnpArrayExperiment-method
Threshold numeric values	threshold
Constructor for TransitionParam class	show,TransitionParam-method TransitionParam TransitionParam,missing-method TransitionParam,numeric-method
Run the Baum-Welch algorithm to update HMM parameters	updateHmmParams
A hidden markov model for detection of germline copy number variants from arrays	VanillaICE
Default viewports for plotting CNV data with lattice-style graphics	viewports
Lattice-style plots for granges and SnpArrayExperiment objects	xygrid xyplotList xyplotList,GRangesList,SnpArrayExperiment-method xyplotList,HmmGRanges,SnpArrayExperiment-method