A Hidden Markov Model for high throughput genotyping arrays

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Documentation for package ‘VanillaICE’ version 1.18.0

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$-method BeadStudioSetList class
$<--method BeadStudioSetList class
BeadStudioSet Constructor for BeadStudioSet class
BeadStudioSetList Constructor for BeadStudioSetList class.
BeadStudioSetList-class BeadStudioSetList class
centerAutosomesAt Center estimates of copy number for autosomes.
copyNumberLimits Constraints for updating the means for the copy number states in the hidden markov model.
emission Methods for Viterbi objects
emission-method Methods for Viterbi objects
hmm Hidden Markov Model methods
hmm-method BeadStudioSetList class
hmm-method Hidden Markov Model methods
hmm-methods Hidden Markov Model methods
hmmBeadStudioSet 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 class
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.
sd Methods for estimating copy number standard deviations.
sd-method Methods for estimating copy number standard deviations.
sd-methods Methods for estimating copy number standard deviations.
Viterbi-methods Methods for Viterbi objects
viterbi2Wrapper Wrapper function for fitting the viterbi algorithm
[-method BeadStudioSetList class
[[-method BeadStudioSetList class