deriveHMM: Derive a standard hidden Markov model from a set of...
In aphid: Analysis with Profile Hidden Markov Models

deriveHMM

R Documentation

Derive a standard hidden Markov model from a set of sequences.

Description

deriveHMM calculates the maximum likelihood hidden Markov model from a list of training sequences, each a vector of residues named according the state from which they were emitted.

Usage

deriveHMM(
  x,
  seqweights = NULL,
  residues = NULL,
  states = NULL,
  modelend = FALSE,
  pseudocounts = "background",
  logspace = TRUE
)

Arguments

`x`	a list of named character vectors representing emissions from the model. The 'names' attribute should represent the hidden state from which each residue was emitted. "DNAbin" and "AAbin" list objects are also supported for modeling DNA or amino acid sequences.
`seqweights`	either NULL (all sequences are given weights of 1) or a numeric vector the same length as `x` representing the sequence weights used to derive the model.
`residues`	either NULL (default; emitted residues are automatically detected from the sequences), a case sensitive character vector specifying the residue alphabet, or one of the character strings "RNA", "DNA", "AA", "AMINO". Note that the default option can be slow for large lists of character vectors. Furthermore, the default setting `residues = NULL` will not detect rare residues that are not present in the sequences, and thus will not assign them emission probabilities in the model. Specifying the residue alphabet is therefore recommended unless x is a "DNAbin" or "AAbin" object.
`states`	either NULL (default; the unique Markov states are automatically detected from the 'names' attributes of the input sequences), or a case sensitive character vector specifying the unique Markov states (or a superset of the unique states) to appear in the model. The latter option is recommended since it saves computation time and ensures that all valid Markov states appear in the model, regardless of their possible absence from the training dataset.
`modelend`	logical indicating whether transition probabilites to the end state of the standard hidden Markov model should be modeled (if applicable). Defaults to FALSE.
`pseudocounts`	character string, either "background", Laplace" or "none". Used to account for the possible absence of certain transition and/or emission types in the input sequences. If `pseudocounts = "background"` (default), pseudocounts are calculated from the background transition and emission frequencies in the training dataset. If `pseudocounts = "Laplace"` one of each possible transition and emission type is added to the training dataset (default). If `pseudocounts = "none"` no pseudocounts are added (not usually recommended, since low frequency transition/emission types may be excluded from the model). Alternatively this argument can be a two-element list containing a matrix of transition pseudocounts as its first element and a matrix of emission pseudocounts as its second. If this option is selected, both matrices must have row and column names corresponding with the residues (column names of emission matrix) and states (row and column names of the transition matrix and row names of the emission matrix). For downstream applications the first row and column of the transition matrix should be named "Begin".
`logspace`	logical indicating whether the emission and transition probabilities in the returned model should be logged. Defaults to TRUE.

Details

This function creates a standard hidden Markov model (object class: "HMM") using the method described in Durbin et al (1998) chapter 3.3. It assumes the state sequence is known (as opposed to the train.HMM function, which is used when the state sequence is unknown) and provided as the names attribute(s) of the input sequences. The output object is a simple list with elements "A" (transition probability matrix) and "E" (emission probability matrix), and the "class" attribute "HMM". The emission matrix has the same number of rows as the number of states, and the same number of columns as the number of unique symbols that can be emitted (i.e. the residue alphabet). The number of rows and columns in the transition probability matrix should be one more the number of states, to include the silent "Begin" state in the first row and column. Despite its name, this state is also used when modeling transitions to the (silent) end state, which are entered in the first column.

Value

an object of class "HMM".

Author(s)

Shaun Wilkinson

References

Durbin R, Eddy SR, Krogh A, Mitchison G (1998) Biological sequence analysis: probabilistic models of proteins and nucleic acids. Cambridge University Press, Cambridge, United Kingdom.