Man pages for chromstaR
Combinatorial and Differential Chromatin State Analysis for ChIP-Seq Data

binned.dataBinned read counts
binReadsConvert aligned reads from various file formats into read...
callPeaksMultivariateFit a Hidden Markov Model to multiple ChIP-seq samples
callPeaksReplicatesFit a multivariate Hidden Markov Model to multiple ChIP-seq...
callPeaksUnivariateFit a Hidden Markov Model to a ChIP-seq sample.
callPeaksUnivariateAllChrFit a Hidden Markov Model to a ChIP-seq sample.
changeMaxPostCutoffAdjust sensitivity of peak detection
changePostCutoffChange the posterior cutoff of a Hidden Markov Model
ChromstarWrapper function for the 'chromstaR' package
chromstaR-objectschromstaR objects
chromstaR-packageCombinatorial and differential chromatin state analysis for...
collapseBinsCollapse consecutive bins
combinatorialStatesGet the (decimal) combinatorial states of a list of...
combinedMultiHMMCombined multivariate HMM object
combineMultivariatesCombine combinatorial states from several Multivariates
conversionConversion of decimal and binary states
enrichment_analysisEnrichment analysis
enrichmentAtAnnotationEnrichment of (combinatorial) states for genomic annotations
experiment.tableExperiment data table
exportFilesExport genome browser uploadable files
exportGRangesAsBedFileExport genome browser viewable files
fixedWidthBinsMake fixed-width bins
genes_rn4Gene coordinates for rn4
genomicFrequenciesFrequencies of combinatorial states
getCombinationsGet combinations
getDistinctColorsGet distinct colors
getStateColorsGet state colors
heatmapCombinationsPlot a heatmap of combinatorial states
heatmapCountCorrelationRead count correlation heatmap
heatmapTransitionProbsHeatmap of transition probabilities
loadHmmsFromFilesLoad 'chromstaR' objects from file
mergeChromsMerge several 'multiHMM's into one object
model.combinedCombined multivariate HMM for demonstration purposes
model.multivariateMultivariate HMM for demonstration purposes
model.univariateUnivariate HMM for demonstration purposes
multiHMMMultivariate HMM object
multivariateSegmentationMultivariate segmentation
plotExpressionOverlap with expression data
plotGenomeBrowser#' Plot a genome browser view #' #' Plot a simple genome...
plotHistogramHistogram of binned read counts with fitted mixture...
plotHistogramsHistograms of binned read counts with fitted mixture...
plottingchromstaR plotting functions
print.combinedMultiHMMPrint combinedMultiHMM object
print.multiHMMPrint multiHMM object
print.uniHMMPrint uniHMM object
readBamFileAsGRangesImport BAM file into GRanges
readBedFileAsGRangesImport BED file into GRanges
readConfigRead chromstaR configuration file
readCustomBedFileRead bed-file into GRanges
removeConditionRemove condition from model
scanBinsizesFind the best bin size for a given dataset
scoreschromstaR scores
simulateMultivariateSimulate multivariate data
simulateReadsFromCountsSimulate read coordinates
simulateUnivariateSimulate univariate data
state.brewerObtain combinatorial states from specification
stateBrewerObtain combinatorial states from experiment table
subsampleNormalize read counts
transitionFrequenciesTransition frequencies of combinatorial states
uniHMMUnivariate HMM object
unis2pseudomultiCombine univariate HMMs to a multivariate HMM
variableWidthBinsMake variable-width bins
writeConfigWrite chromstaR configuration file
zinbinomThe Zero-inflated Negative Binomial Distribution
chromstaR documentation built on Nov. 8, 2020, 8:29 p.m.