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, contHMM |
Class "contHMM" |
initialize,contDist-method |
Generating Objects of Class 'dist' |
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 |
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" |
[[.discDist |
Accessing and Converting Objects of Class "dist" |