A Hidden Markov Model for high throughput genotyping arrays

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Documentation for package ‘VanillaICE’ version 1.16.1

Help Pages

centerAutosomesAt Center estimates of copy number for autosomes.
cnEmission Calculate emission probabilities for total copy number
cnEmission-method Methods for Function 'cnEmission' in Package 'VanillaICE'
cnEmission-methods Methods for Function 'cnEmission' in Package 'VanillaICE'
gtEmission Calculate emission probabilities for genotypes
gtEmission-method Methods for calculating the emission probabilities of diallelic genotypes in Package 'VanillaICE'
gtEmission-methods Methods for calculating the emission probabilities of diallelic genotypes in Package 'VanillaICE'
hmm Application of the Viterbi algorithm to copy number and/or genotype data.
hmm-method A container for storing options for the hidden Markov model
hmm.setup Constructors for HmmOptionList class
HmmOptionList Constructors for HmmOptionList class
HmmOptionList-class A container for storing options for the hidden Markov model
hmmResults Example output from hmm
icePlatforms List platforms for which ICE option is supported.
order-method Methods for oligoSnpSet class
robustSds Calculate robust estimates of the standard deviation
sd Methods for estimating copy number standard deviations.
sd-method Methods for oligoSnpSet class
sd-method Methods for estimating copy number standard deviations.
sd-methods Methods for estimating copy number standard deviations.
xypanel A panel function for plotting copy number versus physical position
xyplot Plot copy number and physical position for a set of genomic intervals.
xyplot-method Plot copy number and physical position for a set of genomic intervals.
xyplot2 Plot copy number and physical position for a set of genomic intervals.
xyplot2-method Plot copy number and physical position for a set of genomic intervals.