VanillaICE: A Hidden Markov Model for high throughput genotyping arrays

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

AuthorRobert Scharpf <rscharpf@jhu.edu>, Kevin Scharpf, and Ingo Ruczinski <ingo@jhsph.edu>
Date of publicationNone
MaintainerRobert Scharpf <rscharpf@jhsph.edu>
LicenseLGPL-2
Version1.36.0

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'

Functions

acf2 Man page
ArrayViews Man page
[,ArrayViews,ANY,ANY,ANY-method Man page
'[',ArrayViews,ANY-method Man page
"[",ArrayViews,ANY-method Man page
ArrayViews-class Man page
$<-,ArrayViews-method Man page
$,ArrayViews-method Man page
ArrayViews,numeric,numeric-method Man page
baf,ArrayViews-method Man page
bafFile Man page
bafFile,ArrayViews-method Man page
baf_means Man page
baf_means<- Man page
baf_means,ArrayViews-method Man page
baf_means,EmissionParam-method Man page
baf_means<-,EmissionParam,numeric-method Man page
baf_means,HmmParam-method Man page
baf_sds Man page
baf_sds<- Man page
baf_sds,EmissionParam-method Man page
baf_sds<-,EmissionParam,numeric-method Man page
baf_sds,HmmParam-method Man page
baf,SnpArrayExperiment-method Man page
baumWelchUpdate Man page
calculateEmission Man page
calculateEmission,list-method Man page
calculateEmission,numeric-method Man page
calculateEmission,RangedSummarizedExperiment-method Man page
cn_means Man page
cn_means<- Man page
cn_means,EmissionParam-method Man page
cn_means<-,EmissionParam,numeric-method Man page
cn_means,HmmParam-method Man page
cn_sds Man page
cn_sds<- Man page
cn_sds,EmissionParam-method Man page
cn_sds<-,EmissionParam,numeric-method Man page
cn_sds,HmmParam-method Man page
cnvFilter Man page
cnvFilter,GRanges-method Man page
cnvFilter,HMMList-method Man page
cnvFilter,HMM-method Man page
cnvSegs Man page
cnvSegs,HmmGRanges-method Man page
cnvSegs,HMMList-method Man page
cnvSegs,HMM-method Man page
colModes Man page
colnames Man page
colnames<- Man page
colnames<-,ArrayViews,character-method Man page
colnames,ArrayViews-method Man page
copyNumber,SnpArrayExperiment-method Man page
CopyNumScanParams Man page
CopyNumScanParams-class Man page
deletion Man page
deletion,HMM-method Man page
dim,ArrayViews-method Man page
doUpdate Man page
dropDuplicatedMapLocs Man page
dropSexChrom Man page
duplication Man page
duplication,HMMList-method Man page
duplication,HMM-method Man page
emission Man page
emission<- Man page
emission<-,HMM-method Man page
emission<-,HmmParam-method Man page
emission,HmmParam-method Man page
emissionParam Man page
emissionParam<- Man page
EmissionParam Man page
emissionParam<-,HmmGRanges,EmissionParam-method Man page
emissionParam,HmmGRanges-method Man page
emissionParam,HMM-method Man page
emissionParam<-,HmmParam,EmissionParam-method Man page
emissionParam,HmmParam-method Man page
EmissionParam,missing-method Man page
EmissionParam,numeric-method Man page
EMupdates Man page
EMupdates,EmissionParam-method Man page
EMupdates,HmmParam-method Man page
FilterParam Man page
FilterParam-class Man page
filters Man page
filters,HMM-method Man page
filters,HmmParam-method Man page
genotypes Man page
genotypes,ArrayViews-method Man page
genotypes,SnpArrayExperiment-method Man page
getExampleSnpExperiment Man page
getHmmParams Man page
getHmmParams,HMM-method Man page
getHmmParams,HmmParam-method Man page
gtFile Man page
gtFile,ArrayViews-method Man page
hemizygous Man page
hemizygous,HMMList-method Man page
hemizygous,HMM-method Man page
HMM Man page
hmm2 Man page
hmm2,ArrayViews-method Man page
hmm2,oligoSnpSet-method Man page
hmm2,SnpArrayExperiment-method Man page
HMM-class Man page
HMMList Man page
HMMList-class Man page
HmmParam Man page
HmmParam,matrix-method Man page
HmmParam,missing-method Man page
hmmResults Man page
HmmTrellisParam Man page
homozygous Man page
homozygous,HMMList-method Man page
homozygous,HMM-method Man page
IdiogramParams Man page
IdiogramParams-class Man page
isHeterozygous Man page
isHeterozygous,ArrayViews-method Man page
isHeterozygous,matrix-method Man page
isHeterozygous,numeric-method Man page
isHeterozygous,SnpArrayExperiment-method Man page
length,LogLik-method Man page
LogLik Man page
LogLik-class Man page
lrr,ArrayViews-method Man page
lrrFile Man page
lrrFile<- Man page
lrrFile<-,ArrayViews-method Man page
lrrFile,ArrayViews-method Man page
lrr,SnpArrayExperiment-method Man page
matrixOrNULL Man page
matrixOrNULL-class Man page
NA_filter Man page
NA_filter,character-method Man page
NA_filter,list-method Man page
NA_filter,numeric-method Man page
NA_filter,oligoSnpSet-method Man page
NA_filter,SnpArrayExperiment-method Man page
ncol,ArrayViews-method Man page
ncol,HmmParam-method Man page
nrow,ArrayViews-method Man page
nrow,HmmParam-method Man page
numberFeatures Man page
numberFeatures,FilterParam-method Man page
numberFeatures,HmmGRanges-method Man page
numberFeatures,HMM-method Man page
parsedPath Man page
parsedPath,ArrayViews-method Man page
parseSourceFile Man page
parseSourceFile,ArrayViews,CopyNumScanParams-method Man page
plot,IdiogramParams,ANY-method Man page
plot,IdiogramParams-method Man page
probability Man page
probability,FilterParam-method Man page
rescale Man page
rowMAD Man page
rowModes Man page
sapply,ArrayViews-method Man page
segs Man page
segs,HMMList-method Man page
segs,HMM-method Man page
show,ArrayViews-method Man page
show,CopyNumScanParams-method Man page
show,EmissionParam-method Man page
show,FilterParam-method Man page
show,HMMList-method Man page
show,HMM-method Man page
show,HmmParam-method Man page
show,IdiogramParams-method Man page
show,LogLik-method Man page
show,TransitionParam-method Man page
show,Viterbi-method Man page
snpArrayAssays Man page
SnpArrayExperiment Man page
SnpArrayExperiment-class Man page
SnpArrayExperiment,matrix-method Man page
SnpArrayExperiment,missing-method Man page
snp_exp Man page
SnpExperiment Man page
SnpExperiment,ArrayViews-method Man page
SnpGRanges Man page
SnpGRanges-class Man page
SnpGRanges,GRanges-method Man page
SnpGRanges,missing-method Man page
sourcePaths Man page
sourcePaths,ArrayViews-method Man page
start,ArrayViews-method Man page
start,oligoSnpSet-method Man page
state,FilterParam-method Man page
state,HmmGRanges-method Man page
state,HMM-method Man page
state-methods Man page
state,Viterbi-method Man page
sweepMode Man page
sweepMode,SnpArrayExperiment-method Man page
threshold Man page
TransitionParam Man page
TransitionParam,missing-method Man page
TransitionParam,numeric-method Man page
unlist,HMMList-method Man page
updateHmmParams Man page
VanillaICE Man page
VanillaICE-package Man page
viewports Man page
xygrid Man page
xyplotList Man page
xyplotList,GRangesList,SnpArrayExperiment-method Man page
xyplotList,HmmGRanges,SnpArrayExperiment-method Man page

Files

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

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