| Safe Haskell | Safe-Inferred |
|---|---|
| Language | Haskell98 |
Bio.MemeData
Description
This module contains a hierarchical data structure for Multiple EM for Motif Elicitation (MEME) results For more information on MEME consult: http://meme.nbcr.net/meme/
- data MemeResult = MemeResult {}
- data TrainingSet = TrainingSet {}
- data MemeAlphabet = MemeAlphabet {}
- data MemeLetter = MemeLetter {}
- data MemeAmbigs = MemeAmbigs {}
- data Sequence = Sequence {}
- data LetterFrequencies = LetterFrequencies {}
- data Model = Model {
- commandLine :: String
- host :: String
- modelType :: String
- nmotifs :: Int
- evalueThreshold :: String
- objectFunction :: String
- minWidth :: Int
- maxWidth :: Int
- minic :: Double
- wg :: Int
- ws :: Int
- endGaps :: String
- minSites :: Int
- maxSites :: Int
- wnSites :: Double
- prob :: Int
- spMap :: String
- spFuzz :: Double
- prior :: String
- beta :: Double
- maxiter :: Int
- distance :: Double
- numSequences :: Int
- numPositions :: Int
- seed :: Int
- seqfrac :: String
- strands :: String
- priorsFile :: String
- reasonForStopping :: String
- backgroundFrequencies :: BackgroundFrequencies
- data BackgroundFrequencies = BackgroundFrequencies {}
- data AlphabetArray = AlphabetArray {}
- data AlphabetArrayValue = AlphabetArrayValue {}
- data Motif = Motif {
- motifId :: String
- motifName :: String
- motifWidth :: Int
- motifSites :: Int
- motifIc :: Double
- motifRe :: Double
- motifLlr :: Int
- motifEvalue :: Double
- motifBayesTreshold :: Double
- motifElapsedTime :: Double
- motifRegularexpression :: String
- motifScores :: Scores
- motifProbabilites :: Propabilities
- motifContributingsites :: [ContributingSite]
- data Scores = Scores {}
- data Propabilities = Propabilities {}
- data AlphabetMatrix = AlphabetMatrix {}
- data ContributingSite = ContributingSite {}
- data Site = Site {}
- data LetterReference = LetterReference {}
- data ScannedSiteSummary = ScannedSiteSummary {
- pThresh :: Double
- scannedSites :: [ScannedSites]
- data ScannedSites = ScannedSites {}
- data ScannedSite = ScannedSite {}
Documentation
data MemeResult Source
Document Root of Meme xml output
Constructors
| MemeResult | |
Fields
| |
Instances
data TrainingSet Source
Training set defines the data used for the motif search
Constructors
| TrainingSet | |
Instances
Constructors
| Sequence | |
Fields
| |
Constructors
| Model | |
Fields
| |
The motifs are predicted by appying the model to the trainingset
Constructors
| Motif | |
Fields
| |
Constructors
| Scores | |
Fields | |
Constructors
| Site | |
Fields | |
data ScannedSiteSummary Source
Scanned sites contain all sites evaluated for possible motifs
Constructors
| ScannedSiteSummary | |
Fields
| |
Instances
data ScannedSite Source
Constructors
| ScannedSite | |
Fields
| |
Instances