# A Hidden Markov Model for high throughput genotyping arrays

## Documentation for package ‘VanillaICE’ version 1.16.1

- DESCRIPTION file.
- Overview of user guides and package vignettes; browse directory.

## 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.