Man pages for VanillaICE
A Hidden Markov Model for high throughput genotyping arrays
| acf2 | Calculate lag10 autocorrelation |
| ArrayViews-class | ArrayViews class, constructor, and methods |
| baumWelchUpdate | Function for updating parameters for emission probabilities |
| calculateEmission | Calculate the emission probabilities for the 6-state HMM |
| cnvFilter | Filter the HMM-derived genomic ranges for copy number... |
| CopyNumScanParams | Parameters for parsing source files containing SNP-array... |
| doUpdate | Helper function to determine whether to update the HMM... |
| dropDuplicatedMapLocs | Drop markers on the same chromosome having the same genomic... |
| dropSexChrom | Filter sex chromosomes |
| emission | Methods to set and get emission probabilities |
| emissionParam | Accessor for parameters used to compute emission... |
| EmissionParam-methods | A parameter class for computing Emission probabilities |
| FilterParam-class | Container for the common criteria used to filtering genomic... |
| filters | Accessor for HMM filter parameters |
| getExampleSnpExperiment | Create an example SnpArrayExperiment from source files... |
| getHmmParams | Accessor for HMM model parameters |
| HMM | Container for the segmented data and the 6-state HMM model... |
| hmm2 | Fit a 6-state HMM to log R ratios and B allele frequencies... |
| HmmGRanges-methods | Accessor for copy number state |
| HMMList | Constructor for 'HMMList' class |
| HMMList-class | Class, constructor, and methods for representing HMM results... |
| HmmParam | Constructor for HmmParam class |
| hmmResults | Example output from the hidden markov model |
| HmmTrellisParam | Constructor for HmmTrellisParam class |
| IdiogramParam-class | Constructor for IdiogramParam objects |
| IdiogramParams-class | Paramater class for plotting idiograms |
| IO | Accessors for objects of class ArrayViews |
| isHeterozygous | Assess whether genotype is heterozygous based on BAFs |
| LogLik | Constructor for LogLik class |
| LogLik-class | Classes and methods for storing/getting log-likelihoods from... |
| LowLevelSummaries | Accessor for SNP genotypes |
| matrixOrNULL-class | A class allowing matrix or NULL objects |
| NA_filter | Remove SNPs with NAs in any of the low-level estimates |
| numberFeatures | The number of SNP/nonpolymorphic probes contained in a... |
| parsedPath | Complete path to directory for keeping parsed files |
| parseSourceFile | Function for parsing GenomeStudio files |
| plotting | Lattice-style plots for granges and SnpArrayExperiment... |
| probability | Accessor for probability filter |
| rescale | Rescale a numeric vector |
| robust-statistics | Robust statistics for matrices |
| segs | Accessor for the HMM segments |
| snpArrayAssays | Create an assays object from log R ratios and B allele... |
| SnpArrayExperiment-class | A RangedSummarizedExperiment-derived class of marker-level... |
| snp_exp | An example SnpArrayExperiment |
| SnpExperiment | Constructor for SnpArrayExperiment |
| SnpGRanges | An extension to GRanges for representing SNPs |
| sourcePaths | Accessor for file paths containing SNP-level summaries |
| start-oligoSnpSet-method | Retrieve genomic location of SNPs |
| state-methods | Accessor for the Viterbi state path |
| sweepMode | Sweep the modal log R ratio (by row or column) from a matrix... |
| threshold | Threshold numeric values |
| TransitionParam | Constructor for TransitionParam class |
| updateHmmParams | Run the Baum-Welch algorithm to update HMM parameters |
| VanillaICE | A hidden markov model for detection of germline copy number... |
| viewports | Default viewports for plotting CNV data with lattice-style... |
| Viterbi-methods | Show method for objects of class 'Viterbi' |
