{ "_id": "6a0f6301acfb0bcc41c5c5e1", "Package": "VanillaICE", "Version": "1.75.0", "Title": "A Hidden Markov Model for high throughput genotyping arrays", "Authors@R": "person(\"Robert\", \"Scharpf\", email=\"rscharpf@jhu.edu\", role=c(\"aut\", \"cre\"))", "Description": "Hidden Markov Models for characterizing chromosomal\nalteration in high throughput SNP arrays.", "Date": "2021-11-21", "Collate": "'AllClasses.R' 'AllGenerics.R' 'datasets.R' 'functions.R'\n'help.R' 'hmm-methods.R' 'methods-ArrayViews.R'\n'methods-CopyNumScanParams.R' 'methods-EmissionParam.R'\n'methods-FilterParam.R' 'methods-HMM.R' 'methods-HMMList.R'\n'methods-HmmGRanges.R' 'methods-HmmParam.R'\n'methods-HmmTrellisParam.R' 'methods-IdiogramParams.R'\n'methods-LogLik.R' 'methods-SnpArrayExperiment.R'\n'methods-SnpDataFrame.R' 'methods-TransitionParam.R'\n'methods-Viterbi.R' 'updates.R' 'zzz.R'", "License": "LGPL-2", "LazyLoad": "yes", "biocViews": "CopyNumberVariation", "Roxygen": "", "RoxygenNote": "7.1.1", 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[ { "page": "acf2", "title": "Calculate lag10 autocorrelation", "topics": [ "acf2" ] }, { "page": "ArrayViews-class", "title": "ArrayViews class, constructor, and methods", "topics": [ "\"[\",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" ] }, { "page": "baumWelchUpdate", "title": "Function for updating parameters for emission probabilities", "topics": [ "baumWelchUpdate" ] }, { "page": "calculateEmission", "title": "Calculate the emission probabilities for the 6-state HMM", "topics": [ "calculateEmission", "calculateEmission,list-method", "calculateEmission,numeric-method", "calculateEmission,RangedSummarizedExperiment-method" ] }, { "page": "EmissionParam-methods", "title": "A parameter class for computing Emission probabilities", "concept": [ "EmissionParam-methods" ], "topics": [ "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" ] }, { "page": "cnvFilter", "title": "Filter the HMM-derived genomic ranges for copy number variants", "topics": [ "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" ] }, { "page": "CopyNumScanParams", "title": "Parameters for parsing source files containing SNP-array processed data, such as GenomeStudio files for the Illumina platform", "topics": [ "CopyNumScanParams", "CopyNumScanParams-class", "show,CopyNumScanParams-method" ] }, { "page": "doUpdate", "title": "Helper function to determine whether to update the HMM parameters via the Baum-Welch algorithm", "topics": [ "doUpdate" ] }, { "page": "dropDuplicatedMapLocs", "title": "Drop markers on the same chromosome having the same genomic coordinates", "topics": [ "dropDuplicatedMapLocs" ] }, { "page": "dropSexChrom", "title": "Filter sex chromosomes", "topics": [ "dropSexChrom" ] }, { "page": "emission", "title": "Methods to set and get emission probabilities", "topics": [ "emission", "emission,HmmParam-method", "emission<-", "emission<-,HMM-method", "emission<-,HmmParam-method" ] }, { "page": "emissionParam", "title": "Accessor for parameters used to compute emission probabilities", "topics": [ "emissionParam", "emissionParam,HMM-method", "emissionParam,HmmGRanges-method", "emissionParam,HmmParam-method", "emissionParam<-", "emissionParam<-,HmmGRanges,EmissionParam-method", "emissionParam<-,HmmParam,EmissionParam-method" ] }, { "page": "FilterParam-class", "title": "Container for the common criteria used to filtering genomic ranges", "topics": [ "FilterParam", "FilterParam-class", "probability,FilterParam-method", "show,FilterParam-method", "state,FilterParam-method" ] }, { "page": "filters", "title": "Accessor for HMM filter parameters", "topics": [ "filters", "filters,HMM-method", "filters,HmmParam-method" ] }, { "page": "LowLevelSummaries", "title": "Accessor for SNP genotypes", "topics": [ "baf,ArrayViews-method", "baf,SnpArrayExperiment-method", "copyNumber,SnpArrayExperiment-method", "genotypes", "genotypes,ArrayViews-method", "genotypes,SnpArrayExperiment-method", "lrr,ArrayViews-method", "lrr,SnpArrayExperiment-method" ] }, { "page": "getExampleSnpExperiment", "title": "Create an example SnpArrayExperiment from source files containing marker-level genomic data that are provided in this package", "topics": [ "getExampleSnpExperiment" ] }, { "page": "getHmmParams", "title": "Accessor for HMM model parameters", "topics": [ "getHmmParams", "getHmmParams,HMM-method", "getHmmParams,HmmParam-method" ] }, { "page": "HMM", "title": "Container for the segmented data and the 6-state HMM model parameters", "topics": [ "HMM", "HMM-class", "show,HMM-method", "state,HMM-method" ] }, { "page": "hmm2", "title": "Fit a 6-state HMM to log R ratios and B allele frequencies estimated from SNP arrays", "topics": [ "hmm2", "hmm2,ArrayViews-method", "hmm2,oligoSnpSet-method", "hmm2,SnpArrayExperiment-method" ] }, { "page": "HMMList", "title": "Constructor for 'HMMList' class", "topics": [ "HMMList" ] }, { "page": "HMMList-class", "title": "Class, constructor, and methods for representing HMM results from multiple samples", "topics": [ "HMMList-class", "show,HMMList-method", "unlist,HMMList-method" ] }, { "page": "HmmParam", "title": "Constructor for HmmParam class", "topics": [ "HmmParam", "HmmParam,matrix-method", "HmmParam,missing-method", "ncol,HmmParam-method", "nrow,HmmParam-method", "show,HmmParam-method" ] }, { "page": "hmmResults", "title": "Example output from the hidden markov model", "topics": [ "hmmResults" ] }, { "page": "HmmTrellisParam", "title": "Constructor for HmmTrellisParam class", "topics": [ "HmmTrellisParam" ] }, { "page": "IdiogramParam-class", "title": "Constructor for IdiogramParam objects", "topics": [ "IdiogramParams", "plot,IdiogramParams,ANY-method", "plot,IdiogramParams-method" ] }, { "page": "IdiogramParams-class", "title": "Paramater class for plotting idiograms", "topics": [ "IdiogramParams-class", "show,IdiogramParams-method" ] }, { "page": "isHeterozygous", "title": "Assess whether genotype is heterozygous based on BAFs", "topics": [ "isHeterozygous", "isHeterozygous,ArrayViews-method", "isHeterozygous,matrix-method", "isHeterozygous,numeric-method", "isHeterozygous,SnpArrayExperiment-method" ] }, { "page": "LogLik", "title": "Constructor for LogLik class", "topics": [ "LogLik" ] }, { "page": "LogLik-class", "title": "Classes and methods for storing/getting log-likelihoods from Viterbi algorithm", "topics": [ "length,LogLik-method", "LogLik-class", "show,LogLik-method" ] }, { "page": "IO", "title": "Accessors for objects of class ArrayViews", "topics": [ "bafFile", "bafFile,ArrayViews-method", "gtFile", "gtFile,ArrayViews-method", "lrrFile", "lrrFile,ArrayViews-method", "lrrFile<-", "lrrFile<-,ArrayViews-method" ] }, { "page": "matrixOrNULL-class", "title": "A class allowing matrix or NULL objects", "topics": [ "matrixOrNULL", "matrixOrNULL-class" ] }, { "page": "NA_filter", "title": "Remove SNPs with NAs in any of the low-level estimates", "topics": [ "NA_filter", "NA_filter,character-method", "NA_filter,list-method", "NA_filter,numeric-method", "NA_filter,oligoSnpSet-method", "NA_filter,SnpArrayExperiment-method" ] }, { "page": "numberFeatures", "title": "The number of SNP/nonpolymorphic probes contained in a genomic interval", "topics": [ "numberFeatures", "numberFeatures,FilterParam-method", "numberFeatures,HMM-method", "numberFeatures,HmmGRanges-method" ] }, { "page": "parsedPath", "title": "Complete path to directory for keeping parsed files", "topics": [ "parsedPath", "parsedPath,ArrayViews-method" ] }, { "page": "parseSourceFile", "title": "Function for parsing GenomeStudio files", "topics": [ "parseSourceFile", "parseSourceFile,ArrayViews,CopyNumScanParams-method" ] }, { "page": "probability", "title": "Accessor for probability filter", "topics": [ "probability" ] }, { "page": "rescale", "title": "Rescale a numeric vector", "topics": [ "rescale" ] }, { "page": "robust-statistics", "title": "Robust statistics for matrices", "topics": [ "colModes", "rowMAD", "rowModes" ] }, { "page": "segs", "title": "Accessor for the HMM segments", "topics": [ "segs", "segs,HMM-method" ] }, { "page": "Viterbi-methods", "title": "Show method for objects of class 'Viterbi'", "topics": [ "show,Viterbi-method" ] }, { "page": "snp_exp", "title": "An example SnpArrayExperiment", "topics": [ "snp_exp" ] }, { "page": "snpArrayAssays", "title": "Create an assays object from log R ratios and B allele frequencies", "topics": [ "snpArrayAssays" ] }, { "page": "SnpArrayExperiment-class", "title": "A RangedSummarizedExperiment-derived class of marker-level SNP array data for copy number inference", "topics": [ "SnpArrayExperiment", "SnpArrayExperiment,matrix-method", "SnpArrayExperiment,missing-method", "SnpArrayExperiment-class" ] }, { "page": "SnpExperiment", "title": "Constructor for SnpArrayExperiment", "topics": [ "SnpExperiment", "SnpExperiment,ArrayViews-method" ] }, { "page": "SnpGRanges", "title": "An extension to GRanges for representing SNPs", "topics": [ "SnpGRanges", "SnpGRanges,GRanges-method", "SnpGRanges,missing-method", "SnpGRanges-class" ] }, { "page": "sourcePaths", "title": "Accessor for file paths containing SNP-level summaries", "topics": [ "sourcePaths", "sourcePaths,ArrayViews-method" ] }, { "page": "start-oligoSnpSet-method", "title": "Retrieve genomic location of SNPs", "topics": [ "start,oligoSnpSet-method" ] }, { "page": "state-methods", "title": "Accessor for the Viterbi state path", "topics": [ "state,Viterbi-method", "state-methods" ] }, { "page": "HmmGRanges-methods", "title": "Accessor for 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