initBdClust: Initialization of bidirectional Clustering
In STAN: The Genomic STate ANnotation Package

Initialization of bidirectional Clustering

1	initBdClust(obs, dStates = 0, uStates = 0, method, directedObs = rep(0, ncol(obs[[1]])), sizeFactors = matrix(1, nrow = length(obs), ncol = ncol(obs[[1]])), sharedCov = FALSE, dirFlags = NULL)

`obs`	The observations. A list of one or more entries containing the observation matrix (`numeric`) for the samples (e.g. chromosomes).
`dStates`	The number of directed states.
`uStates`	The number of undirected states.
`method`	Emission distribution of the model. One out of c("NegativeBinomial", "PoissonLogNormal", "NegativeMultinomial", "ZINegativeBinomial", "Poisson", "Bernoulli", "Gaussian", "IndependentGaussian")
`directedObs`	Integer vector defining the directionality (or strand-specificity) of the data tracks. Undirected (non-strand-specific) data tracks (e.g. ChIP) are indicated indicated by '0'. Directed (strand-specific) data tracks are indicated by increasing pairs of integers. For instance c(0,0,0,1,1,2,2): The first three data tracks are undirected, followed by two pairs of directed measurements.
`sizeFactors`	Library size factors for Emissions PoissonLogNormal or NegativeBinomial as a length(obs) x ncol(obs[[1]]) matrix.
`sharedCov`	If TRUE, (co-)variance of (Independent)Gaussian is shared over states. Only applicable to 'Gaussian' or 'IndependentGaussian' emissions. Default: FALSE.
`dirFlags`	The flag sequence is needed when a bdHMM is fitted on undirected data (e.g.) ChIP only. It is a `list` of `character` vectors indication for each position its knwon directionality. U allows all states. F allows undirected states and states in forward direction. R allows undirected states and states in reverse direction.