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-method | Computation of Forward and Backward Variables |
baumWelch | Baum-Welch Algorithm |
baumWelch-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-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,contHMM | Class "contHMM" |
initialize-method | Generating Objects of Class 'dist' |
initialize-method | Generate Objects of Class 'hmm' |
length-method | Accessing Objects of Class "contHMM" |
length-method | Accessing and Converting Objects of Class "dist" |
logSum | Calculate log(x + y) from log(x) and log(y) |
new-method | Generating Objects of Class 'dist' |
new-method | Generate Objects of Class 'hmm' |
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-method | Sample Observations from Probability Distribution |
sampleSeq | Generate Observation Sequence from HMM |
sampleSeq-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-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-method | Calculate Most Likely State Sequence Using the Viterbi Algorithm |
viterbiEM | Efficient Estimation of HMM Parameters |
viterbiTraining | Estimate HMM Parameters Using Viterbi Training |
viterbiTraining-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" |