Biobase.Types.Bitscore

Bit scores as used by different algorithms in bioinformatics, linguistics, and probably elsewhere.

Basically, the base-2 logarithm of the probability of the input given the model vs the probability of the input given the null model.

S = log_2 (P(seq|model) / P(seq|null))

Documentation

newtype Bitscore

Bit score; behaves like a double (deriving Num). In particular, the algebraic operations behave as expected Bitscore a + Bitscore b == Bitscore (a+b).

Currently geared towards use as in Infernal and HMMER.

Infernal users guide, p.42: log-odds score in log_2 (aka bits).

Constructors

Bitscore

Fields

• getBitscore :: Double

Instances

Eq Bitscore

Defined in Biobase.Types.Bitscore

Methods

(==) :: Bitscore -> Bitscore -> Bool

(/=) :: Bitscore -> Bitscore -> Bool

Fractional Bitscore

Defined in Biobase.Types.Bitscore

Methods

(/) :: Bitscore -> Bitscore -> Bitscore

recip :: Bitscore -> Bitscore

fromRational :: Rational -> Bitscore

Num Bitscore

Defined in Biobase.Types.Bitscore

Methods

(+) :: Bitscore -> Bitscore -> Bitscore

(-) :: Bitscore -> Bitscore -> Bitscore

(*) :: Bitscore -> Bitscore -> Bitscore

negate :: Bitscore -> Bitscore

abs :: Bitscore -> Bitscore

signum :: Bitscore -> Bitscore

fromInteger :: Integer -> Bitscore

Ord Bitscore

Defined in Biobase.Types.Bitscore

Methods

compare :: Bitscore -> Bitscore -> Ordering

(<) :: Bitscore -> Bitscore -> Bool

(<=) :: Bitscore -> Bitscore -> Bool

(>) :: Bitscore -> Bitscore -> Bool

(>=) :: Bitscore -> Bitscore -> Bool

max :: Bitscore -> Bitscore -> Bitscore

min :: Bitscore -> Bitscore -> Bitscore

Read Bitscore

Defined in Biobase.Types.Bitscore

Methods

readsPrec :: Int -> ReadS Bitscore

readList :: ReadS [Bitscore]

readPrec :: ReadPrec Bitscore

readListPrec :: ReadPrec [Bitscore]

Show Bitscore

Defined in Biobase.Types.Bitscore

Methods

showsPrec :: Int -> Bitscore -> ShowS

show :: Bitscore -> String

showList :: [Bitscore] -> ShowS

Generic Bitscore

Defined in Biobase.Types.Bitscore

Associated Types

type Rep Bitscore :: Type -> Type

Methods

from :: Bitscore -> Rep Bitscore x

to :: Rep Bitscore x -> Bitscore

NumericLimits Bitscore

Defined in Biobase.Types.Bitscore

Methods

minFinite :: Bitscore

maxFinite :: Bitscore

Semiring Bitscore

Defined in Biobase.Types.Bitscore

Methods

plus :: Bitscore -> Bitscore -> Bitscore

zero :: Bitscore

times :: Bitscore -> Bitscore -> Bitscore

one :: Bitscore

NFData Bitscore

Defined in Biobase.Types.Bitscore

Methods

rnf :: Bitscore -> ()

Hashable Bitscore

Defined in Biobase.Types.Bitscore

Methods

hashWithSalt :: Int -> Bitscore -> Int

hash :: Bitscore -> Int

ToJSON Bitscore

Defined in Biobase.Types.Bitscore

Methods

toJSON :: Bitscore -> Value

toEncoding :: Bitscore -> Encoding

toJSONList :: [Bitscore] -> Value

toEncodingList :: [Bitscore] -> Encoding

FromJSON Bitscore

Defined in Biobase.Types.Bitscore

Methods

parseJSON :: Value -> Parser Bitscore

parseJSONList :: Value -> Parser [Bitscore]

Binary Bitscore

Defined in Biobase.Types.Bitscore

Methods

put :: Bitscore -> Put

get :: Get Bitscore

putList :: [Bitscore] -> Put

Serialize Bitscore

Defined in Biobase.Types.Bitscore

Methods

put :: Putter Bitscore

get :: Get Bitscore

Default Bitscore

A default bitscore of "-infinity", but with 10-1 wiggle room.

TODO Check out the different "defaults" Infernal uses

Defined in Biobase.Types.Bitscore

Methods

def :: Bitscore

Unbox Bitscore

Defined in Biobase.Types.Bitscore

Vector Vector Bitscore

Defined in Biobase.Types.Bitscore

Methods

basicUnsafeFreeze :: PrimMonad m => Mutable Vector (PrimState m) Bitscore -> m (Vector Bitscore)

basicUnsafeThaw :: PrimMonad m => Vector Bitscore -> m (Mutable Vector (PrimState m) Bitscore)

basicLength :: Vector Bitscore -> Int

basicUnsafeSlice :: Int -> Int -> Vector Bitscore -> Vector Bitscore

basicUnsafeIndexM :: Monad m => Vector Bitscore -> Int -> m Bitscore

basicUnsafeCopy :: PrimMonad m => Mutable Vector (PrimState m) Bitscore -> Vector Bitscore -> m ()

elemseq :: Vector Bitscore -> Bitscore -> b -> b

MVector MVector Bitscore

Defined in Biobase.Types.Bitscore

Methods

basicLength :: MVector s Bitscore -> Int

basicUnsafeSlice :: Int -> Int -> MVector s Bitscore -> MVector s Bitscore

basicOverlaps :: MVector s Bitscore -> MVector s Bitscore -> Bool

basicUnsafeNew :: PrimMonad m => Int -> m (MVector (PrimState m) Bitscore)

basicInitialize :: PrimMonad m => MVector (PrimState m) Bitscore -> m ()

basicUnsafeReplicate :: PrimMonad m => Int -> Bitscore -> m (MVector (PrimState m) Bitscore)

basicUnsafeRead :: PrimMonad m => MVector (PrimState m) Bitscore -> Int -> m Bitscore

basicUnsafeWrite :: PrimMonad m => MVector (PrimState m) Bitscore -> Int -> Bitscore -> m ()

basicClear :: PrimMonad m => MVector (PrimState m) Bitscore -> m ()

basicSet :: PrimMonad m => MVector (PrimState m) Bitscore -> Bitscore -> m ()

basicUnsafeCopy :: PrimMonad m => MVector (PrimState m) Bitscore -> MVector (PrimState m) Bitscore -> m ()

basicUnsafeMove :: PrimMonad m => MVector (PrimState m) Bitscore -> MVector (PrimState m) Bitscore -> m ()

basicUnsafeGrow :: PrimMonad m => MVector (PrimState m) Bitscore -> Int -> m (MVector (PrimState m) Bitscore)

type Rep Bitscore

Defined in Biobase.Types.Bitscore

type Rep Bitscore = D1 (MetaData "Bitscore" "Biobase.Types.Bitscore" "BiobaseTypes-0.2.0.0-I16yhMsM66JLeHk27CPQMF" True) (C1 (MetaCons "Bitscore" PrefixI True) (S1 (MetaSel (Just "getBitscore") NoSourceUnpackedness NoSourceStrictness DecidedLazy) (Rec0 Double)))

newtype Vector Bitscore

Defined in Biobase.Types.Bitscore

newtype Vector Bitscore = V_Bitscore (Vector Double)

newtype MVector s Bitscore

Defined in Biobase.Types.Bitscore

newtype MVector s Bitscore = MV_Bitscore (MVector s Double)

prob2Score :: Double -> Double -> Bitscore

Given a null model and a probability, calculate the corresponding BitScore.

TODO x<=epsilon ?

score2Prob :: Double -> Bitscore -> Double

Given a null model and a BitScore return the corresponding probability.