| Safe Haskell | None |
|---|---|
| Language | Haskell2010 |
Biobase.SubstMatrix
Synopsis
- mkANuc3SubstMat :: TranslationTable (Letter DNA n) (Letter AA n) -> AASubstMat t (DiscLogOdds k) n -> ANuc3SubstMat t (Letter AA n, DiscLogOdds k) n n
- fromFileOrCached :: (MonadIO m, MonadError String m) => FilePath -> m (AASubstMat t (DiscLogOdds Unknown) a)
- mkProbabilityMatrix :: Double -> AASubstMat t (DiscLogOdds k) n -> AASubstMat t (Log (Probability NotNormalized Double)) n
Documentation
mkANuc3SubstMat :: TranslationTable (Letter DNA n) (Letter AA n) -> AASubstMat t (DiscLogOdds k) n -> ANuc3SubstMat t (Letter AA n, DiscLogOdds k) n n Source #
The usual substitution matrix, but here with a codon and an amino acid to be compared.
The resulting AA are tagged with the name type from the DNA n.
TODO Definitely use the correct upper bound constants here!
fromFileOrCached :: (MonadIO m, MonadError String m) => FilePath -> m (AASubstMat t (DiscLogOdds Unknown) a) Source #
This function does the following:
1. check if fname is a file, and if so try to load it.
2. if not, check if fname happens to be the name of one of the known PAM/BLOSUM tables.
mkProbabilityMatrix :: Double -> AASubstMat t (DiscLogOdds k) n -> AASubstMat t (Log (Probability NotNormalized Double)) n Source #
Turn log-odds into log-probabilities. Normalizes over the whole set of values in the matrix.