# A Hidden Markov Model for high throughput genotyping arrays

## Documentation for package ‘VanillaICE’ version 1.26.1

- DESCRIPTION file.
- User guides, package vignettes and other documentation.
- Package NEWS.

## Help Pages

$-method | BeadStudioSetList methods
$<--method | BeadStudioSetList methods
BeadStudioSet | Constructor for BeadStudioSet class
BeadStudioSetList | Constructor for BeadStudioSetList class.
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
hmmBafLrrSet2 | HMM functions for oligoSnpSet and BeadStudioSet containers
hmmBafLrrSetList2 | HMM functions for oligoSnpSet and BeadStudioSet containers
hmmOligoSnpSet2 | HMM functions for oligoSnpSet and BeadStudioSet containers
hmmResults | Example output from hmm
hmmSnpSet2 | Function for fitting a HMM to SnpSet containers
hmmSnpSetIce | 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