baf-method |
Accessor for SNP genotypes |
bafFile |
Accessor for parsed file(s) containing low level summaries for copy number analysis |
bafFile-method |
Accessor for parsed file(s) containing low level summaries for copy number analysis |
baf_means |
A parameter class for computing Emission probabilities |
baf_means-method |
ArrayViews class, constructor, and methods |
baf_means-method |
A parameter class for computing Emission probabilities |
baf_means<- |
A parameter class for computing Emission probabilities |
baf_means<--method |
A parameter class for computing Emission probabilities |
baf_sds |
A parameter class for computing Emission probabilities |
baf_sds-method |
A parameter class for computing Emission probabilities |
baf_sds<- |
A parameter class for computing Emission probabilities |
baf_sds<--method |
A parameter class for computing Emission probabilities |
baumWelchUpdate |
Function for updating parameters for emission probabilities |
calculateEmission |
Calculate the emission probabilities for the 6-state HMM |
calculateEmission-method |
Calculate the emission probabilities for the 6-state HMM |
cnvFilter |
Filter the HMM-derived genomic ranges for copy number variants |
cnvFilter-method |
Filter the HMM-derived genomic ranges for copy number variants |
cnvSegs |
Filter the HMM-derived genomic ranges for copy number variants |
cnvSegs-method |
Filter the HMM-derived genomic ranges for copy number variants |
cn_means |
A parameter class for computing Emission probabilities |
cn_means-method |
A parameter class for computing Emission probabilities |
cn_means<- |
A parameter class for computing Emission probabilities |
cn_means<--method |
A parameter class for computing Emission probabilities |
cn_sds |
A parameter class for computing Emission probabilities |
cn_sds-method |
A parameter class for computing Emission probabilities |
cn_sds<- |
A parameter class for computing Emission probabilities |
cn_sds<--method |
A parameter class for computing Emission probabilities |
colModes |
Robust statistics for matrices |
colnames<- |
ArrayViews class, constructor, and methods |
colnames<--method |
ArrayViews class, constructor, and methods |
constrainMu2 |
Constraints for updating the means of the copy number states |
constrainSd2 |
Constraints for updating the means of the copy number states |
copyNumber-method |
Accessor for SNP genotypes |
copyNumberLimits |
Constraints for updating the means of the copy number states |
CopyNumScanParams |
Parameters for parsing source files containing SNP-array processed data, such as GenomeStudio files for the Illumina platform |
CopyNumScanParams-class |
Parameters for parsing source files containing SNP-array processed data, such as GenomeStudio files for the Illumina platform |
hemizygous |
Filter the HMM-derived genomic ranges for copy number variants |
hemizygous-method |
Filter the HMM-derived genomic ranges for copy number variants |
HMM |
Container for the segmented data and the 6-state HMM model parameters |
hmm |
Deprecated functions in the VanillaICE package |
HMM-class |
Container for the segmented data and the 6-state HMM model parameters |
hmm-method |
Deprecated functions in the VanillaICE package |
hmm2 |
Fit a 6-state HMM to log R ratios and B allele frequencies estimated from SNP arrays |
hmm2-method |
Fit a 6-state HMM to log R ratios and B allele frequencies estimated from SNP arrays |
HMMList |
Constructor for 'HMMList' class |
HMMList-class |
Class, constructor, and methods for representing HMM results from multiple samples |
HmmParam |
Constructor for HmmParam class |
HmmParam-method |
Constructor for HmmParam class |
hmmResults |
Example output from the hidden markov model |
HmmTrellisParam |
Constructor for HmmTrellisParam class |
homozygous |
Filter the HMM-derived genomic ranges for copy number variants |
homozygous-method |
Filter the HMM-derived genomic ranges for copy number variants |
sapply-method |
ArrayViews class, constructor, and methods |
segs |
Accessor for the HMM segments |
segs-method |
Filter the HMM-derived genomic ranges for copy number variants |
segs-method |
Accessor for the HMM segments |
show-method |
ArrayViews class, constructor, and methods |
show-method |
Parameters for parsing source files containing SNP-array processed data, such as GenomeStudio files for the Illumina platform |
show-method |
A parameter class for computing Emission probabilities |
show-method |
Container for the common criteria used to filtering genomic ranges |
show-method |
Container for the segmented data and the 6-state HMM model parameters |
show-method |
Class, constructor, and methods for representing HMM results from multiple samples |
show-method |
Constructor for HmmParam class |
show-method |
Paramater class for plotting idiograms |
show-method |
Classes and methods for storing/getting log-likelihoods from Viterbi algorithm |
show-method |
Constructor for TransitionParam class |
show-method |
Show method for objects of class 'Viterbi' |
snpArrayAssays |
Create an assays object from log R ratios and B allele frequencies |
SnpArrayExperiment |
A SummarizedExperiment-derived class of marker-level SNP array data for copy number inference |
SnpArrayExperiment-class |
A SummarizedExperiment-derived class of marker-level SNP array data for copy number inference |
SnpArrayExperiment-method |
A SummarizedExperiment-derived class of marker-level SNP array data for copy number inference |
SnpExperiment |
Constructor for SnpArrayExperiment |
SnpExperiment-method |
Constructor for SnpArrayExperiment |
SnpGRanges |
An extension to GRanges for representing SNPs |
SnpGRanges-class |
An extension to GRanges for representing SNPs |
SnpGRanges-method |
An extension to GRanges for representing SNPs |
snp_exp |
An example SnpArrayExperiment |
sourcePaths |
Accessor for file paths containing SNP-level summaries |
sourcePaths-method |
Accessor for file paths containing SNP-level summaries |
start-method |
ArrayViews class, constructor, and methods |
start-method |
Retrieve genomic location of SNPs |
state-method |
Container for the common criteria used to filtering genomic ranges |
state-method |
Container for the segmented data and the 6-state HMM model parameters |
state-method |
Accessor for copy number state |
state-method |
Accessor for the Viterbi state path |
state-methods |
Accessor for the Viterbi state path |
sweepMode |
Sweep the modal log R ratio (by row or column) from a matrix of log R ratios |
sweepMode-method |
Sweep the modal log R ratio (by row or column) from a matrix of log R ratios |
"["-method |
ArrayViews class, constructor, and methods |
'$'-method |
ArrayViews class, constructor, and methods |
'['-method |
ArrayViews class, constructor, and methods |
'[<-'-method |
ArrayViews class, constructor, and methods |
[-method |
ArrayViews class, constructor, and methods |
[[-method |
Subset method for deprecated 'oligoSetList' |