Combinatorial and Differential Chromatin State Analysis for ChIP-Seq Data


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Documentation for package ‘chromstaR’ version 1.0.0

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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.
changePostCutoff Change the false discovery rate 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
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
multi.hmm Multivariate HMM object
multiHMM Multivariate HMM object
multivariateSegmentation Multivariate segmentation
multivariate_model Multivariate HMM for demonstration purposes
plotEnrichCountHeatmap Enrichment analysis
plotExpression Overlap with expression data
plotFoldEnrichHeatmap Enrichment analysis
plotFoldEnrichment Enrichment analysis
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
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
rzinbinom The Zero-inflated Negative Binomial Distribution
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
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