# Combinatorial and Differential Chromatin State Analysis for ChIP-Seq Data

## Documentation for package ‘chromstaR’ version 1.4.0

- DESCRIPTION file.
- User guides, package vignettes and other documentation.
- Package NEWS.

## Help Pages

chromstaR-package | Combinatorial and differential chromatin state analysis for ChIP-seq data
bin2dec | Conversion of decimal and binary states
binned.data | Binned read counts
binning | Convert aligned reads from various file formats into read counts in equidistant bins
binReads | Convert aligned reads from various file formats into read counts in equidistant bins
callPeaksMultivariate | Fit a Hidden Markov Model to multiple ChIP-seq samples
callPeaksReplicates | Fit a multivariate Hidden Markov Model to multiple ChIP-seq replicates
callPeaksUnivariate | Fit a Hidden Markov Model to a ChIP-seq sample.
callPeaksUnivariateAllChr | Fit a Hidden Markov Model to a ChIP-seq sample.
changeFDR | Change the false discovery rate of a Hidden Markov Model
changePostCutoff | Change the posterior cutoff of a Hidden Markov Model
Chromstar | Wrapper function for the 'chromstaR' package
chromstaR | Combinatorial and differential chromatin state analysis for ChIP-seq data
chromstaR-objects | chromstaR objects
collapseBins | Collapse consecutive bins
combinatorialStates | Get the (decimal) combinatorial states of a list of univariate HMM models
combinedHMM | Combined multivariate HMM object
combinedMultiHMM | Combined multivariate HMM object
combined_model | Combined multivariate HMM for demonstration purposes
combineMultivariates | Combine combinatorial states from several Multivariates
conversion | Conversion of decimal and binary states
dec2bin | Conversion of decimal and binary states
differentialScoreMax | chromstaR scores
differentialScoreSum | chromstaR scores
dzinbinom | The Zero-inflated Negative Binomial Distribution
enrichmentAtAnnotation | Enrichment of (combinatorial) states for genomic annotations
enrichment_analysis | Enrichment analysis
experiment.table | Experiment data table
exportCombinations | Export genome browser uploadable files
exportCounts | Export genome browser uploadable files
exportFiles | Export genome browser uploadable files
exportGRangesAsBedFile | Export genome browser viewable files
exportPeaks | Export genome browser uploadable files
fixedWidthBins | Make fixed-width bins
genes_rn4 | Gene coordinates for rn4
genomicFrequencies | Frequencies of combinatorial states
getCombinations | Get combinations
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
multi.hmm | Multivariate HMM object
multiHMM | Multivariate HMM object
multivariateSegmentation | Multivariate segmentation
multivariate_model | Multivariate HMM for demonstration purposes
plotEnrichCountHeatmap | Enrichment analysis
plotEnrichment | Enrichment analysis
plotExpression | Overlap with expression data
plotFoldEnrichHeatmap | Enrichment analysis
plotGenomeBrowser | Plot a genome browser view
plotHistogram | Histogram of binned read counts with fitted mixture distribution
plotHistograms | Histograms of binned read counts with fitted mixture distribution
plotKaryogram | Plot a karyogram with read counts and univariate peak calls
plotting | chromstaR plotting functions
print.combinedMultiHMM | Print combinedMultiHMM object
print.multiHMM | Print multiHMM object
print.uniHMM | Print uniHMM object
pzinbinom | The Zero-inflated Negative Binomial Distribution
qzinbinom | The Zero-inflated Negative Binomial Distribution
readBamFileAsGRanges | Import BAM file into GRanges
readBedFileAsGRanges | Import BED file into GRanges
readConfig | Read chromstaR configuration file
readCustomBedFile | Read bed-file into GRanges
removeCondition | Remove condition from model
rzinbinom | The Zero-inflated Negative Binomial Distribution
scanBinsizes | Find the best bin size for a given dataset
scores | chromstaR scores
simulateMultivariate | Simulate multivariate data
simulateReadsFromCounts | Simulate read coordinates
simulateUnivariate | Simulate univariate 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
uni.hmm | Univariate HMM object
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