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' |

Embedding an R snippet on your website

Add the following code to your website.

For more information on customizing the embed code, read Embedding Snippets.