VanillaICE: A Hidden Markov Model for high throughput genotyping arrays

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Hidden Markov Models for characterizing chromosomal alterations in high throughput SNP arrays.

Author
Robert Scharpf <rscharpf@jhu.edu>, Kevin Scharpf, and Ingo Ruczinski <ingo@jhsph.edu>
Date of publication
None
Maintainer
Robert Scharpf <rscharpf@jhsph.edu>
License
LGPL-2
Version
1.36.0

View on Bioconductor

Man pages

acf2
Calculate lag10 autocorrelation
ArrayViews-class
ArrayViews class, constructor, and methods
baumWelchUpdate
Function for updating parameters for emission probabilities
calculateEmission
Calculate the emission probabilities for the 6-state HMM
cnvFilter
Filter the HMM-derived genomic ranges for copy number...
CopyNumScanParams
Parameters for parsing source files containing SNP-array...
doUpdate
Helper function to determine whether to update the HMM...
dropDuplicatedMapLocs
Drop markers on the same chromosome having the same genomic...
dropSexChrom
Filter sex chromosomes
emission
Methods to set and get emission probabilities
emissionParam
Accessor for parameters used to compute emission...
EmissionParam-methods
A parameter class for computing Emission probabilities
FilterParam-class
Container for the common criteria used to filtering genomic...
filters
Accessor for HMM filter parameters
getExampleSnpExperiment
Create an example SnpArrayExperiment from source files...
getHmmParams
Accessor for HMM model parameters
HMM
Container for the segmented data and the 6-state HMM model...
hmm2
Fit a 6-state HMM to log R ratios and B allele frequencies...
HmmGRanges-methods
Accessor for copy number state
HMMList
Constructor for 'HMMList' class
HMMList-class
Class, constructor, and methods for representing HMM results...
HmmParam
Constructor for HmmParam class
hmmResults
Example output from the hidden markov model
HmmTrellisParam
Constructor for HmmTrellisParam class
IdiogramParam-class
Constructor for IdiogramParam objects
IdiogramParams-class
Paramater class for plotting idiograms
IO
Accessors for objects of class ArrayViews
isHeterozygous
Assess whether genotype is heterozygous based on BAFs
LogLik
Constructor for LogLik class
LogLik-class
Classes and methods for storing/getting log-likelihoods from...
LowLevelSummaries
Accessor for SNP genotypes
matrixOrNULL-class
A class allowing matrix or NULL objects
NA_filter
Remove SNPs with NAs in any of the low-level estimates
numberFeatures
The number of SNP/nonpolymorphic probes contained in a...
parsedPath
Complete path to directory for keeping parsed files
parseSourceFile
Function for parsing GenomeStudio files
plotting
Lattice-style plots for granges and SnpArrayExperiment...
probability
Accessor for probability filter
rescale
Rescale a numeric vector
robust-statistics
Robust statistics for matrices
segs
Accessor for the HMM segments
snpArrayAssays
Create an assays object from log R ratios and B allele...
SnpArrayExperiment-class
A RangedSummarizedExperiment-derived class of marker-level...
snp_exp
An example SnpArrayExperiment
SnpExperiment
Constructor for SnpArrayExperiment
SnpGRanges
An extension to GRanges for representing SNPs
sourcePaths
Accessor for file paths containing SNP-level summaries
start-oligoSnpSet-method
Retrieve genomic location of SNPs
state-methods
Accessor for the Viterbi state path
sweepMode
Sweep the modal log R ratio (by row or column) from a matrix...
threshold
Threshold numeric values
TransitionParam
Constructor for TransitionParam class
updateHmmParams
Run the Baum-Welch algorithm to update HMM parameters
VanillaICE
A hidden markov model for detection of germline copy number...
viewports
Default viewports for plotting CNV data with lattice-style...
Viterbi-methods
Show method for objects of class 'Viterbi'

Files in this package

VanillaICE/CHANGES
VanillaICE/DESCRIPTION
VanillaICE/NAMESPACE
VanillaICE/NEWS
VanillaICE/R
VanillaICE/R/AllClasses.R
VanillaICE/R/AllGenerics.R
VanillaICE/R/datasets.R
VanillaICE/R/functions.R
VanillaICE/R/help.R
VanillaICE/R/hmm-methods.R
VanillaICE/R/methods-ArrayViews.R
VanillaICE/R/methods-CopyNumScanParams.R
VanillaICE/R/methods-EmissionParam.R
VanillaICE/R/methods-FilterParam.R
VanillaICE/R/methods-HMM.R
VanillaICE/R/methods-HMMList.R
VanillaICE/R/methods-HmmGRanges.R
VanillaICE/R/methods-HmmParam.R
VanillaICE/R/methods-HmmTrellisParam.R
VanillaICE/R/methods-IdiogramParams.R
VanillaICE/R/methods-LogLik.R
VanillaICE/R/methods-SnpArrayExperiment.R
VanillaICE/R/methods-SnpDataFrame.R
VanillaICE/R/methods-TransitionParam.R
VanillaICE/R/methods-Viterbi.R
VanillaICE/R/updates.R
VanillaICE/R/zzz.R
VanillaICE/build
VanillaICE/build/vignette.rds
VanillaICE/changelog
VanillaICE/data
VanillaICE/data/snp_exp.rda
VanillaICE/inst
VanillaICE/inst/CITATION
VanillaICE/inst/NEWS.Rd
VanillaICE/inst/doc
VanillaICE/inst/doc/VanillaICE.R
VanillaICE/inst/doc/VanillaICE.Rnw
VanillaICE/inst/doc/VanillaICE.pdf
VanillaICE/inst/doc/crlmmDownstream.R
VanillaICE/inst/doc/crlmmDownstream.Rnw
VanillaICE/inst/doc/crlmmDownstream.pdf
VanillaICE/inst/extdata
VanillaICE/inst/extdata/FinalReport1664.txt
VanillaICE/inst/extdata/FinalReport1675.txt
VanillaICE/inst/extdata/FinalReport1686.txt
VanillaICE/inst/extdata/FinalReport6841.txt
VanillaICE/inst/extdata/FinalReport6872.txt
VanillaICE/inst/extdata/FinalReport6903.txt
VanillaICE/inst/extdata/SNP_info.csv
VanillaICE/inst/extdata/sample_data.csv
VanillaICE/inst/extdata/snp_exp.rda
VanillaICE/inst/illumina
VanillaICE/inst/illumina/illuminaEx.txt
VanillaICE/inst/scripts
VanillaICE/inst/scripts/crlmmDownstream.Rnw
VanillaICE/inst/scripts/crlmmDownstream.pdf
VanillaICE/inst/scripts/runcrlmm.R
VanillaICE/inst/test
VanillaICE/inst/test/crlmmDownstream.Rnw
VanillaICE/inst/testing
VanillaICE/inst/unitTests
VanillaICE/inst/unitTests/Makefile
VanillaICE/inst/unitTests/TestData.R
VanillaICE/inst/unitTests/test_ArrayViews.R
VanillaICE/inst/unitTests/test_BeadStudioSet.R
VanillaICE/inst/unitTests/test_FilterParam.R
VanillaICE/inst/unitTests/test_HmmGRanges.R
VanillaICE/inst/unitTests/test_HmmParam.R
VanillaICE/inst/unitTests/test_SnpArrayExperiment.R
VanillaICE/inst/unitTests/test_SnpGRanges.R
VanillaICE/inst/unitTests/test_SummarizedExperiment.R
VanillaICE/inst/unitTests/test_acf2.R
VanillaICE/inst/unitTests/test_constraints.R
VanillaICE/inst/unitTests/test_hmm.R
VanillaICE/inst/unitTests/test_loess.R
VanillaICE/inst/unitTests/test_oligoSetList.R
VanillaICE/inst/unitTests/test_rowMAD.R
VanillaICE/inst/unitTests/test_scaleBy.R
VanillaICE/inst/unitTests/test_sweepMode.R
VanillaICE/inst/unitTests/test_viterbi.R
VanillaICE/man
VanillaICE/man/ArrayViews-class.Rd
VanillaICE/man/CopyNumScanParams.Rd
VanillaICE/man/EmissionParam-methods.Rd
VanillaICE/man/FilterParam-class.Rd
VanillaICE/man/HMM.Rd
VanillaICE/man/HMMList-class.Rd
VanillaICE/man/HMMList.Rd
VanillaICE/man/HmmGRanges-methods.Rd
VanillaICE/man/HmmParam.Rd
VanillaICE/man/HmmTrellisParam.Rd
VanillaICE/man/IO.Rd
VanillaICE/man/IdiogramParam-class.Rd
VanillaICE/man/IdiogramParams-class.Rd
VanillaICE/man/LogLik-class.Rd
VanillaICE/man/LogLik.Rd
VanillaICE/man/LowLevelSummaries.Rd
VanillaICE/man/NA_filter.Rd
VanillaICE/man/SnpArrayExperiment-class.Rd
VanillaICE/man/SnpExperiment.Rd
VanillaICE/man/SnpGRanges.Rd
VanillaICE/man/TransitionParam.Rd
VanillaICE/man/VanillaICE.Rd
VanillaICE/man/Viterbi-methods.Rd
VanillaICE/man/acf2.Rd
VanillaICE/man/baumWelchUpdate.Rd
VanillaICE/man/calculateEmission.Rd
VanillaICE/man/cnvFilter.Rd
VanillaICE/man/doUpdate.Rd
VanillaICE/man/dropDuplicatedMapLocs.Rd
VanillaICE/man/dropSexChrom.Rd
VanillaICE/man/emission.Rd
VanillaICE/man/emissionParam.Rd
VanillaICE/man/filters.Rd
VanillaICE/man/getExampleSnpExperiment.Rd
VanillaICE/man/getHmmParams.Rd
VanillaICE/man/hmm2.Rd
VanillaICE/man/hmmResults.Rd
VanillaICE/man/isHeterozygous.Rd
VanillaICE/man/matrixOrNULL-class.Rd
VanillaICE/man/numberFeatures.Rd
VanillaICE/man/parseSourceFile.Rd
VanillaICE/man/parsedPath.Rd
VanillaICE/man/plotting.Rd
VanillaICE/man/probability.Rd
VanillaICE/man/rescale.Rd
VanillaICE/man/robust-statistics.Rd
VanillaICE/man/segs.Rd
VanillaICE/man/snpArrayAssays.Rd
VanillaICE/man/snp_exp.Rd
VanillaICE/man/sourcePaths.Rd
VanillaICE/man/start-oligoSnpSet-method.Rd
VanillaICE/man/state-methods.Rd
VanillaICE/man/sweepMode.Rd
VanillaICE/man/threshold.Rd
VanillaICE/man/updateHmmParams.Rd
VanillaICE/man/viewports.Rd
VanillaICE/src
VanillaICE/src/Makevars
VanillaICE/src/rinit.c
VanillaICE/src/viterbi.c
VanillaICE/tests
VanillaICE/tests/doRUnit.R
VanillaICE/vignettes
VanillaICE/vignettes/VanillaICE.Rnw
VanillaICE/vignettes/crlmmDownstream.Rnw
VanillaICE/vignettes/ice.bib