bioinformatics-toolkit-0.10.0: A collection of bioinformatics tools

Safe Haskell	None
Language	Haskell2010

Bio.Motif.Merge

Synopsis

mergePWM :: (PWM, PWM, Int) -> PWM
mergePWMWeighted :: (PWM, [Int]) -> (PWM, [Int]) -> Int -> (PWM, [Int])
dilute :: (PWM, [Int]) -> PWM
trim :: Bkgd -> Double -> PWM -> PWM
mergeTree :: AlignFn -> Dendrogram Motif -> PWM
mergeTreeWeighted :: AlignFn -> Dendrogram Motif -> (PWM, [Int])
iterativeMerge :: AlignFn -> Double -> [Motif] -> [([ByteString], PWM, [Int])]
buildTree :: AlignFn -> [Motif] -> Dendrogram Motif
cutTreeBy :: Double -> Double -> ([Dendrogram a] -> Bool) -> Dendrogram a -> [Dendrogram a]

Documentation

mergePWM :: (PWM, PWM, Int) -> PWM Source #

mergePWMWeighted Source #

Arguments

:: (PWM, [Int])	pwm and weights at each position
-> (PWM, [Int])
-> Int	shift
-> (PWM, [Int])

dilute :: (PWM, [Int]) -> PWM Source #

dilute positions in a PWM that are associated with low weights

trim :: Bkgd -> Double -> PWM -> PWM Source #

mergeTree :: AlignFn -> Dendrogram Motif -> PWM Source #

mergeTreeWeighted :: AlignFn -> Dendrogram Motif -> (PWM, [Int]) Source #

iterativeMerge Source #

Arguments

:: AlignFn
-> Double
-> [Motif]	Motifs to be merged. Motifs must have unique name.
-> [([ByteString], PWM, [Int])]

buildTree :: AlignFn -> [Motif] -> Dendrogram Motif Source #

build a guide tree from a set of motifs

cutTreeBy Source #

Arguments

:: Double	start
-> Double	step
-> ([Dendrogram a] -> Bool)
-> Dendrogram a
-> [Dendrogram a]