| baf-method |
Accessor for SNP genotypes |
| bafFile |
Accessors for objects of class ArrayViews |
| bafFile-method |
Accessors for objects of class ArrayViews |
| 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 |
| colnames<- |
ArrayViews class, constructor, and methods |
| colnames<--method |
ArrayViews class, constructor, and methods |
| copyNumber-method |
Accessor for SNP genotypes |
| 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-class |
Container for the segmented data and the 6-state HMM model parameters |
| 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 RangedSummarizedExperiment-derived class of marker-level SNP array data for copy number inference |
| SnpArrayExperiment-class |
A RangedSummarizedExperiment-derived class of marker-level SNP array data for copy number inference |
| SnpArrayExperiment-method |
A RangedSummarizedExperiment-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 |