Man pages for Bioconductor-mirror/VanillaICE
A Hidden Markov Model for high throughput genotyping arrays

acf2Calculate lag10 autocorrelation
ArrayViews-classArrayViews class, constructor, and methods
baumWelchUpdateFunction for updating parameters for emission probabilities
calculateEmissionCalculate the emission probabilities for the 6-state HMM
cnvFilterFilter the HMM-derived genomic ranges for copy number...
CopyNumScanParamsParameters for parsing source files containing SNP-array...
doUpdateHelper function to determine whether to update the HMM...
dropDuplicatedMapLocsDrop markers on the same chromosome having the same genomic...
dropSexChromFilter sex chromosomes
emissionMethods to set and get emission probabilities
emissionParamAccessor for parameters used to compute emission...
EmissionParam-methodsA parameter class for computing Emission probabilities
FilterParam-classContainer for the common criteria used to filtering genomic...
filtersAccessor for HMM filter parameters
getExampleSnpExperimentCreate an example SnpArrayExperiment from source files...
getHmmParamsAccessor for HMM model parameters
HMMContainer for the segmented data and the 6-state HMM model...
hmm2Fit a 6-state HMM to log R ratios and B allele frequencies...
HmmGRanges-methodsAccessor for copy number state
HMMListConstructor for 'HMMList' class
HMMList-classClass, constructor, and methods for representing HMM results...
HmmParamConstructor for HmmParam class
hmmResultsExample output from the hidden markov model
HmmTrellisParamConstructor for HmmTrellisParam class
IdiogramParam-classConstructor for IdiogramParam objects
IdiogramParams-classParamater class for plotting idiograms
IOAccessors for objects of class ArrayViews
isHeterozygousAssess whether genotype is heterozygous based on BAFs
LogLikConstructor for LogLik class
LogLik-classClasses and methods for storing/getting log-likelihoods from...
LowLevelSummariesAccessor for SNP genotypes
matrixOrNULL-classA class allowing matrix or NULL objects
NA_filterRemove SNPs with NAs in any of the low-level estimates
numberFeaturesThe number of SNP/nonpolymorphic probes contained in a...
parsedPathComplete path to directory for keeping parsed files
parseSourceFileFunction for parsing GenomeStudio files
plottingLattice-style plots for granges and SnpArrayExperiment...
probabilityAccessor for probability filter
rescaleRescale a numeric vector
robust-statisticsRobust statistics for matrices
segsAccessor for the HMM segments
snpArrayAssaysCreate an assays object from log R ratios and B allele...
SnpArrayExperiment-classA RangedSummarizedExperiment-derived class of marker-level...
snp_expAn example SnpArrayExperiment
SnpExperimentConstructor for SnpArrayExperiment
SnpGRangesAn extension to GRanges for representing SNPs
sourcePathsAccessor for file paths containing SNP-level summaries
start-oligoSnpSet-methodRetrieve genomic location of SNPs
state-methodsAccessor for the Viterbi state path
sweepModeSweep the modal log R ratio (by row or column) from a matrix...
thresholdThreshold numeric values
TransitionParamConstructor for TransitionParam class
updateHmmParamsRun the Baum-Welch algorithm to update HMM parameters
VanillaICEA hidden markov model for detection of germline copy number...
viewportsDefault viewports for plotting CNV data with lattice-style...
Viterbi-methodsShow method for objects of class 'Viterbi'
Bioconductor-mirror/VanillaICE documentation built on July 1, 2017, 6:34 a.m.