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**chromstaR**: Combinatorial and Differential Chromatin State Analysis for ChIP-Seq Data**combined_model**: Combined multivariate HMM for demonstration purposes

# Combined multivariate HMM for demonstration purposes

### Description

A `combinedMultiHMM`

object for demonstration purposes in examples of package chromstaR.

### Format

A `combinedMultiHMM`

object.

### Examples

1 2 3 4 | ```
## Get an example combinedMultiHMM
file <- system.file("data","combined_mode-differential.RData",
package="chromstaR")
model <- get(load(file))
``` |

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- binned.data: Binned read counts
- binReads: Convert aligned reads from various file formats into read...
- callPeaksMultivariate: Fit a Hidden Markov Model to multiple ChIP-seq samples
- callPeaksReplicates: Fit a multivariate Hidden Markov Model to multiple ChIP-seq...
- callPeaksUnivariate: Fit a Hidden Markov Model to a ChIP-seq sample.
- callPeaksUnivariateAllChr: Fit a Hidden Markov Model to a ChIP-seq sample.
- changePostCutoff: Change the false discovery rate of a Hidden Markov Model
- Chromstar: Wrapper function for the 'chromstaR' package
- chromstaR-objects: chromstaR objects
- chromstaR-package: Combinatorial and differential chromatin state analysis for...
- collapseBins: Collapse consecutive bins
- combinatorialStates: Get the (decimal) combinatorial states of a list of...
- combined_model: Combined multivariate HMM for demonstration purposes
- combinedMultiHMM: Combined multivariate HMM object
- combineMultivariates: Combine combinatorial states from several Multivariates
- conversion: Conversion of decimal and binary states
- enrichment_analysis: Enrichment analysis
- enrichmentAtAnnotation: Enrichment of (combinatorial) states for genomic annotations
- experiment.table: Experiment data table
- exportBinnedData: Export genome browser viewable files
- exportCombinedMultivariate: Export genome browser viewable files
- exportGRangesAsBedFile: Export genome browser viewable files
- exportMultivariate: Export genome browser viewable files
- exportUnivariates: Export genome browser viewable files
- fixedWidthBins: Make fixed-width bins
- genomicFrequencies: Frequencies of combinatorial states
- getDistinctColors: Get distinct colors
- getStateColors: Get state colors
- heatmapCombinations: Plot a heatmap of combinatorial states
- heatmapCountCorrelation: Read count correlation heatmap
- heatmapTransitionProbs: Heatmap of transition probabilities
- loadHmmsFromFiles: Load 'chromstaR' objects from file
- mergeChroms: Merge several 'multiHMM's into one object
- multiHMM: Multivariate HMM object
- multivariate_model: Multivariate HMM for demonstration purposes
- multivariateSegmentation: Multivariate segmentation
- plotExpression: Overlap with expression data
- plotHistogram: Histogram of binned read counts with fitted mixture...
- plotHistograms: Histograms of binned read counts with fitted mixture...
- plotKaryogram: Plot a karyogram with read counts and univariate peak calls
- plotting: chromstaR plotting functions
- readBamFileAsGRanges: Import BAM file into GRanges
- readBedFileAsGRanges: Import BED file into GRanges
- readConfig: Read chromstaR configuration file
- readCustomBedFile: Read bed-file into GRanges
- scanBinsizes: Find the best bin size for a given dataset
- scores: chromstaR scores
- simulateReads: Simulate read coordinates
- simulateUnivariate: Simulate data
- state.brewer: Obtain combinatorial states from specification
- stateBrewer: Obtain combinatorial states from experiment table
- subsample: Normalize read counts
- transitionFrequencies: Transition frequencies of combinatorial states
- uniHMM: Univariate HMM object
- unis2pseudomulti: Combine univariate HMMs to a multivariate HMM
- variableWidthBins: Make variable-width bins
- writeConfig: Write chromstaR configuration file
- zinbinom: The Zero-inflated Negative Binomial Distribution