Man pages for chromstaR
Combinatorial and Differential Chromatin State Analysis for ChIP-Seq Data
| 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. |
| changeMaxPostCutoff | Adjust sensitivity of peak detection |
| changePostCutoff | Change the posterior cutoff 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... |
| 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 |
| exportFiles | Export genome browser uploadable files |
| exportGRangesAsBedFile | Export genome browser viewable 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 |
| model.combined | Combined multivariate HMM for demonstration purposes |
| model.multivariate | Multivariate HMM for demonstration purposes |
| model.univariate | Univariate HMM for demonstration purposes |
| multiHMM | Multivariate HMM object |
| multivariateSegmentation | Multivariate segmentation |
| plotExpression | Overlap with expression data |
| plotGenomeBrowser | #' Plot a genome browser view #' #' Plot a simple genome... |
| plotHistogram | Histogram of binned read counts with fitted mixture... |
| plotHistograms | Histograms of binned read counts with fitted mixture... |
| plotting | chromstaR plotting functions |
| print.combinedMultiHMM | Print combinedMultiHMM object |
| print.multiHMM | Print multiHMM object |
| print.uniHMM | Print uniHMM object |
| 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 |
| 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 |
| 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 |
