Package: VanillaICE 1.69.0
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:
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VanillaICE.pdf |VanillaICE.html✨
VanillaICE/json (API)
NEWS
| # Install 'VanillaICE' in R: |
| install.packages('VanillaICE', repos = c('https://bioc.r-universe.dev', 'https://cloud.r-project.org')) |
- snp_exp - An example SnpArrayExperiment
On BioConductor:VanillaICE-1.69.0(bioc 3.21)VanillaICE-1.68.0(bioc 3.20)
This package does not link to any Github/Gitlab/R-forge repository. No issue tracker or development information is available.
Last updated 23 days agofrom:6af9e70b6e. Checks:OK: 1 NOTE: 1 ERROR: 7. Indexed: yes.
| Target | Result | Date |
|---|---|---|
| Doc / Vignettes | OK | Oct 31 2024 |
| R-4.5-win-x86_64 | ERROR | Oct 31 2024 |
| R-4.5-linux-x86_64 | NOTE | Oct 31 2024 |
| R-4.4-win-x86_64 | ERROR | Oct 31 2024 |
| R-4.4-mac-x86_64 | ERROR | Oct 31 2024 |
| R-4.4-mac-aarch64 | ERROR | Oct 31 2024 |
| R-4.3-win-x86_64 | ERROR | Oct 31 2024 |
| R-4.3-mac-x86_64 | ERROR | Oct 31 2024 |
| R-4.3-mac-aarch64 | ERROR | Oct 31 2024 |
Exports:acf2ArrayViewsbafbaf_meansbaf_means<-baf_sdsbaf_sds<-bafFilebaumWelchUpdatecalculateEmissioncn_meanscn_means<-cn_sdscn_sds<-cnvFiltercnvSegscolModescolnamescolnames<-copyNumberCopyNumScanParamsdeletiondoUpdatedropDuplicatedMapLocsdropSexChromduplicationemissionemission<-emissionParamEmissionParamemissionParam<-EMupdatesFilterParamfiltersgenotypesgetExampleSnpExperimentgetHmmParamsgtFilehemizygousHMMhmm2HMMListHmmParamHmmTrellisParamhomozygousIdiogramParamsisHeterozygousLogLiklrrlrrFilelrrFile<-NA_filterncolnrownumberFeaturesparsedPathparseSourceFileplotprobabilityrescalerowMADrowModessapplysegsshowsnpArrayAssaysSnpArrayExperimentSnpExperimentSnpGRangessourcePathsstartstatesweepModethresholdTransitionParamupdateHmmParamsviewportsxygridxyplotList
Dependencies:abindaffyioaskpassbase64beanplotBHBiobaseBiocGenericsBiocIOBiocManagerBiocParallelBiostringsbitbit64bitopsblobBSgenomeBSgenome.Hsapiens.UCSC.hg18cachemclicodetoolscpp11crayoncrlmmcurldata.tableDBIDelayedArrayellipsefastmapffforeachformatRfutile.loggerfutile.optionsgenericsGenomeInfoDbGenomeInfoDbDataGenomicAlignmentsGenomicRangesgluehttrilluminaioIRangesiteratorsjsonlitelambda.rlatticelifecyclelimmaMatrixMatrixGenericsmatrixStatsmemoisemimemvtnormoligoClassesopensslpkgconfigplogrpreprocessCoreR6RcppRcppEigenRCurlrestfulrRhtslibrjsonrlangRsamtoolsRSQLitertracklayerS4ArraysS4VectorssnowSparseArraystatmodSummarizedExperimentsysUCSC.utilsvctrsVGAMXMLXVectoryamlzlibbioc
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 |
