![[R logo]](../../../doc/html/logo.jpg)
| tileHMM-package | Hidden Markov Models for ChIP-on-Chip Analysis |
| as.data.frame.discDist | Accessing and Converting Objects of Class "dist" |
| as.matrix.discDist | Accessing and Converting Objects of Class "dist" |
| as.vector.discDist | Accessing and Converting Objects of Class "dist" |
| backward | Computation of Forward and Backward Variables |
| backward,hmm-method | Computation of Forward and Backward Variables |
| baumWelch | Baum-Welch Algorithm |
| baumWelch,hmm,list-method | Baum-Welch Algorithm |
| contDist-class | Class "contDist" |
| contHMM-access | Accessing Objects of Class "contHMM" |
| contHMM-class | Class "contHMM" |
| discDist-class | Class "discDist" |
| dist-class | Class "dist" |
| forward | Computation of Forward and Backward Variables |
| forward,hmm-method | 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 Data |
| initialize,contDist-method | Generating Objects of Class 'dist' |
| initialize,contHMM | Class "contHMM" |
| initialize,contHMM-method | Generate Objects of Class 'hmm' |
| initialize,discDist-method | Generating Objects of Class 'dist' |
| initialize,tDist-method | Generating Objects of Class 'dist' |
| length,discDist-method | Accessing and Converting Objects of Class "dist" |
| length,hmm-method | Accessing Objects of Class "contHMM" |
| logSum | Calculate log(x + y) from log(x) and log(y) |
| new,contDist-method | Generating Objects of Class 'dist' |
| new,contHMM-method | Generate Objects of Class 'hmm' |
| new,discDist-method | Generating Objects of Class 'dist' |
| new,tDist-method | Generating Objects of Class 'dist' |
| plot | Plotting of "contDist" Objects |
| plot.contDist | Plotting of "contDist" Objects |
| plot.contHMM | Plotting of "contDist" Objects |
| plot.tDist | 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 |
| sampleObs,discDist,numeric-method | Sample Observations from Probability Distribution |
| sampleObs,tDist,numeric-method | Sample Observations from Probability Distribution |
| sampleSeq | Generate Observation Sequence from HMM |
| sampleSeq,contHMM,numeric-method | Generate Observation Sequence from HMM |
| shrinkt.st | Calculate 'Shrinkage t' Statistic |
| simChIP | Simulated ChIP-on-Chip Data |
| states | State Names of Hidden Markov Model |
| states,hmm-method | State Names of Hidden Markov Model |
| tDist-class | Class "tDist" |
| tileHMM | Hidden Markov Models for ChIP-on-Chip Analysis |
| viterbi | Calculate Most Likely State Sequence Using the Viterbi Algorithm |
| viterbi,hmm-method | Calculate Most Likely State Sequence Using the Viterbi Algorithm |
| viterbiEM | Efficient Estimation of HMM Parameters |
| viterbiTraining | Estimate HMM Parameters Using Viterbi Training |
| viterbiTraining,hmm,list-method | Estimate HMM Parameters Using Viterbi Training |
| [.contDist | Accessing and Converting Objects of Class "dist" |
| [.contHMM | Accessing Objects of Class "contHMM" |
| [.discDist | Accessing and Converting Objects of Class "dist" |
| [.tDist | Accessing and Converting Objects of Class "dist" |
| [<-.contDist | Accessing and Converting Objects of Class "dist" |
| [<-.tDist | Accessing and Converting Objects of Class "dist" |
| [[.discDist | Accessing and Converting Objects of Class "dist" |