A Hidden Markov Model for high throughput genotyping arrays

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Documentation for package ‘VanillaICE’ version 1.20.3

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$-method BeadStudioSetList methods
$<--method BeadStudioSetList methods
BeadStudioSet Constructor for BeadStudioSet class
BeadStudioSetList Constructor for BeadStudioSetList class.
constructBafLrrSetListFrom Construct a chromosome-list container from a CNSet object
constructOligoSetListFrom Construct a chromosome-list container from a CNSet object
copyNumberLimits Constraints for updating the means for the copy number states in the hidden markov model.
dims-method BeadStudioSetList methods
dims-method Methods for oligoSetList class
emission Methods for Viterbi objects
emission-method Methods for Viterbi objects
hmm Hidden Markov Model methods
hmm-method Hidden Markov Model methods
hmm-methods Hidden Markov Model methods
hmmBeadStudioSet HMM functions for oligoSnpSet and BeadStudioSet containers
hmmBeadStudioSetList HMM functions for oligoSnpSet and BeadStudioSet containers
hmmOligoSetList HMM functions for oligoSnpSet and BeadStudioSet containers
hmmOligoSnpSet HMM functions for oligoSnpSet and BeadStudioSet containers
hmmResults Example output from hmm
hmmSnpSet Function for fitting a HMM to SnpSet containers
icePlatforms List platforms for which ICE option is supported.
length-method BeadStudioSetList methods
read.bsfiles Read BeadStudio/GenomeStudio processed data.
rescale Rescale a numeric vector
robustSds Calculate robust estimates of the standard deviation
rowMAD Calculate the median absolute deviation for each row in a matrix.
Viterbi-methods Methods for Viterbi objects
viterbi2Wrapper Wrapper function for fitting the viterbi algorithm
[-method BeadStudioSetList methods
[[-method BeadStudioSetList methods
[[-method Methods for oligoSetList class
[[<-,BafLrrSetList,ANY,ANY,BafLrrSet BeadStudioSetList methods
[[<--method BeadStudioSetList methods