Man pages for plbaldoni/epigrahmm
Epigenomic R-based analysis with hidden Markov models
| addOffsets | Add offsets to epigraHMMDataSet |
| callPatterns | Extract posterior probabilities (or combinatorial patterns)... |
| callPeaks | Summarize peak calls and optionally create a BED 6+3 file in... |
| 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 |
| estimateTransitionProb | Estimate transition probability from a sequence of integers |
| expStep | E-step of HMM (forward-backward probability + posterior... |
| helas3 | ENCODE ChIP-seq broad data from Helas3 cell line |
| info | Get information about peak calling results |
| initializer | Initializer of epigraHMM |
| maxStepProb | M-step (maximization w.r.t. initial and transition... |
| normalizeCounts | Normalize counts |
| plotCounts | Create a plot with the results from epigraHMM |
| plotPatterns | Create a plot of differerential patterns posterior... |
| segmentGenome | Segmentation of a genome in non-overlapping windows |
| simulateMarkovChain | Simulates a Markov Chain of length 'n' given a matrix of... |
