Man pages for tileHMM
Hidden Markov Models for ChIP-on-Chip Analysis
| baumWelch | Baum-Welch Algorithm |
| contDist-class | Class "contDist" |
| contHMM-access | Accessing Objects of Class "contHMM" |
| contHMM-class | Class "contHMM" |
| discDist-class | Class "discDist" |
| dist-access | Accessing and Converting Objects of Class "dist" |
| dist-class | Class "dist" |
| forward | Computation of Forward and Backward Variables |
| generate.data | Generate Simulated Dataset |
| getHMM | Create HMM from Parameter Values |
| gff2index | Extract Probe Calls from GFF File |
| hmm-class | Class "hmm" |
| hmm.setup | Create HMM from Initial Parameter Estimates Obtained from... |
| initializeDist-methods | Generating Objects of Class 'dist' |
| initializeHMM-methods | Generate Objects of Class 'hmm' |
| internals | Internal Functions |
| logSum | Calculate log(x + y) from log(x) and log(y) |
| plot | Plotting of "contDist" Objects |
| posterior | Calculate Posterior Probability for States of HMM |
| reg2gff | Converting Information about Enriched Regions into GFF Format |
| region.length | Determine Length of Positive and Negative Regions |
| region.position | Identify Enriched Regions |
| remove.short | Post-Processing of "tileHMM" Results |
| sampleObs | Sample Observations from Probability Distribution |
| sampleSeq | Generate Observation Sequence from HMM |
| shrinkt.st | Calculate 'Shrinkage t' Statistic |
| simChIP | Simulated ChIP-on-Chip Data |
| states | State Names of Hidden Markov Model |
| tDist-class | Class "tDist" |
| tileHMM-package | Hidden Markov Models for ChIP-on-Chip Analysis |
| viterbi | Calculate Most Likely State Sequence Using the Viterbi... |
| viterbiEM | Efficient Estimation of HMM Parameters |
| viterbiTraining | Estimate HMM Parameters Using Viterbi Training |
