STrand-specific ANnotation of genomic data

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Documentation for package ‘STAN’ version 1.0.0

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STAN-package STrand-specific ANnotation of genomic data
.bdHMM This class is a generic container for bidirectional Hidden Markov Models.
.HMM This class is a generic container for Hidden Markov Models.
.HMMEmission This class is a generic container for different emission functions of Hidden Markov Models.
bdHMM Create a bdHMM object
bdHMM-class This class is a generic container for bidirectional Hidden Markov Models.
bdhmm_ex Initial bdHMM for the Quick-Start example in the vignette
example The data for the Quick-Start example in the vignette
fitHMM Fit a Hidden Markov Model
flags Pre-computed flag sequence for the Quick-Start example in the vignette
getPosterior Calculate posterior state distribution.
getViterbi Calculate the most likely state path
HMM Create a HMM object
HMM-class This class is a generic container for Hidden Markov Models.
HMMEmission Create a HMMEmission object
HMMEmission-class This class is a generic container for different emission functions of Hidden Markov Models.
hmm_ex Initial HMM for the Quick-Start example in the vignette
humanCD4T_flags_ex Pre-defined flag sequence for the human CD4T-cell example
humanCD4T_ideogramChr7 Ideogram track of human chromosome 7 for the human CD4T-cell example
humanCD4T_initCovs Pre-computed initial estimates of the covairances for the human CD4T-cell example
humanCD4T_initMeans Pre-computed initial estimates of the means for the human CD4T-cell example
humanCD4T_probeAnno_ex Genomic positions of processed signal for the human CD4T-cell example
humanCD4T_signal_ex Processed ChIP-Seq signal for the human CD4T-cell example
humanCD4T_ucscGenes UCSC gene annotation for the human CD4T-cell example
observations Observation sequence of the Quick-Start example in the vignette
yeastTF_databychrom_ex Processed ChIP-on-chip data for yeast TF example
yeastTF_initCovs Pre-computed initial estimates of the covairances for yeast TF example
yeastTF_initMeans Pre-computed initial estimates of the means for yeast TF example
yeastTF_probeAnno_ex Genomic positions of the ChIP-on-chip data for yeast TF example
yeastTF_SGDGenes SGD annotation for the yeast TF example