Epigenomic R-based analysis with hidden Markov models

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Documentation for package ‘epigraHMM’ version 1.0.3

• DESCRIPTION file.
• User guides, package vignettes and other documentation.

Help Pages

addOffsets	Add offsets to epigraHMMDataSet
callPeaks	Summarize peak calls and optionally create a BED 6+3 file in broadPeak format for visualization
cleanCounts	Remove effects from covariates of interest
controlEM	Control parameters for the EM algorithm from epigraHMM
epigraHMM	Perform peak calling of epigenomic data sets
epigraHMMDataSetFromBam	Create a epigraHMMDataSet from a set of BAM files
epigraHMMDataSetFromMatrix	Create a epigraHMMDataSet from matrices of counts
initializer	Initializer of epigraHMM
normalizeCounts	Normalize counts
plotCounts	Create a plot with the results from epigraHMM
plotPatterns	Create a plot of differerential patterns posterior probabilities from epigraHMM
segmentGenome	Segmentation of a genome in non-overlapping windows