tileHMM: Hidden Markov Models for ChIP-on-Chip Analysis

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Methods and classes to build HMMs that are suitable for the analysis of ChIP-chip data. The provided parameter estimation methods include the Baum-Welch algorithm and Viterbi training as well as a combination of both.

Author
Peter Humburg [aut, cre]
Date of publication
2015-07-03 00:25:58
Maintainer
Peter Humburg <peter.humburg@gmail.com>
License
GPL (>= 2)
Version
1.0-7

View on CRAN

Man pages

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

Files in this package

tileHMM
tileHMM/inst
tileHMM/inst/COPYING
tileHMM/inst/CITATION
tileHMM/inst/doc
tileHMM/inst/doc/tileHMM.pdf
tileHMM/inst/doc/tileHMM.Rnw
tileHMM/inst/doc/tileHMM.R
tileHMM/src
tileHMM/src/tilehmm_lib.c
tileHMM/src/tilehmm_lib.h
tileHMM/NAMESPACE
tileHMM/NEWS.md
tileHMM/data
tileHMM/data/simChIP.rda
tileHMM/data/datalist
tileHMM/R
tileHMM/R/utils.R
tileHMM/R/hmm.R
tileHMM/R/dist.R
tileHMM/vignettes
tileHMM/vignettes/tileHMM.Rnw
tileHMM/README.md
tileHMM/MD5
tileHMM/build
tileHMM/build/vignette.rds
tileHMM/DESCRIPTION
tileHMM/man
tileHMM/man/states.Rd
tileHMM/man/remove.short.Rd
tileHMM/man/forward.Rd
tileHMM/man/dist-class.Rd
tileHMM/man/viterbiEM.Rd
tileHMM/man/tileHMM-package.Rd
tileHMM/man/hmm-class.Rd
tileHMM/man/reg2gff.Rd
tileHMM/man/viterbiTraining.Rd
tileHMM/man/getHMM.Rd
tileHMM/man/dist-access.Rd
tileHMM/man/viterbi.Rd
tileHMM/man/logSum.Rd
tileHMM/man/tDist-class.Rd
tileHMM/man/contHMM-class.Rd
tileHMM/man/simChIP.Rd
tileHMM/man/hmm.setup.Rd
tileHMM/man/region.length.Rd
tileHMM/man/internals.Rd
tileHMM/man/initializeHMM-methods.Rd
tileHMM/man/contDist-class.Rd
tileHMM/man/initializeDist-methods.Rd
tileHMM/man/gff2index.Rd
tileHMM/man/sampleObs.Rd
tileHMM/man/shrinkt.st.Rd
tileHMM/man/generate.data.Rd
tileHMM/man/baumWelch.Rd
tileHMM/man/contHMM-access.Rd
tileHMM/man/posterior.Rd
tileHMM/man/plot.Rd
tileHMM/man/sampleSeq.Rd
tileHMM/man/region.position.Rd
tileHMM/man/discDist-class.Rd