| Safe Haskell | None |
|---|---|
| Language | Haskell2010 |
Bio.Data.Bed.Types
Synopsis
- class BEDLike b where
- class BEDLike b => BEDConvert b where
- asBed :: ByteString -> Int -> Int -> b
- fromLine :: ByteString -> b
- toLine :: b -> ByteString
- convert :: BEDLike b' => b' -> b
- data BED = BED {}
- data BED3 = BED3 {}
- data BEDGraph = BEDGraph {}
- bdgValue :: Lens' BEDGraph Double
- data NarrowPeak = NarrowPeak {}
- npSignal :: Lens' NarrowPeak Double
- npPvalue :: Lens' NarrowPeak (Maybe Double)
- npQvalue :: Lens' NarrowPeak (Maybe Double)
- npPeak :: Lens' NarrowPeak (Maybe Int)
- data BroadPeak = BroadPeak {}
- bpSignal :: Lens' BroadPeak Double
- bpPvalue :: Lens' BroadPeak (Maybe Double)
- bpQvalue :: Lens' BroadPeak (Maybe Double)
- data BEDExt bed a = BEDExt {}
- _bed :: forall bed a bed. Lens (BEDExt bed a) (BEDExt bed a) bed bed
- _data :: forall bed a a. Lens (BEDExt bed a) (BEDExt bed a) a a
- type BEDTree a = HashMap ByteString (IntervalMap Int a)
- newtype Sorted b = Sorted {
- fromSorted :: b
Documentation
class BEDLike b where Source #
A class representing BED-like data, e.g., BED3, BED6 and BED12. BED format uses 0-based index (see documentation).
Methods
chrom :: Lens' b ByteString Source #
Field lens
chromStart :: Lens' b Int Source #
chromEnd :: Lens' b Int Source #
name :: Lens' b (Maybe ByteString) Source #
score :: Lens' b (Maybe Int) Source #
strand :: Lens' b (Maybe Bool) Source #
Return the size of a bed region.
Instances
| BEDLike BEDGraph Source # | |
Defined in Bio.Data.Bed.Types | |
| BEDLike BED3 Source # | |
Defined in Bio.Data.Bed.Types | |
| BEDLike BED Source # | |
| BEDLike NarrowPeak Source # | |
Defined in Bio.Data.Bed.Types Methods chrom :: Lens' NarrowPeak ByteString Source # chromStart :: Lens' NarrowPeak Int Source # chromEnd :: Lens' NarrowPeak Int Source # name :: Lens' NarrowPeak (Maybe ByteString) Source # score :: Lens' NarrowPeak (Maybe Int) Source # strand :: Lens' NarrowPeak (Maybe Bool) Source # size :: NarrowPeak -> Int Source # | |
| BEDLike BroadPeak Source # | |
Defined in Bio.Data.Bed.Types | |
| BEDLike bed => BEDLike (BEDExt bed a) Source # | |
Defined in Bio.Data.Bed.Types Methods chrom :: Lens' (BEDExt bed a) ByteString Source # chromStart :: Lens' (BEDExt bed a) Int Source # chromEnd :: Lens' (BEDExt bed a) Int Source # name :: Lens' (BEDExt bed a) (Maybe ByteString) Source # score :: Lens' (BEDExt bed a) (Maybe Int) Source # | |
class BEDLike b => BEDConvert b where Source #
Methods
asBed :: ByteString -> Int -> Int -> b Source #
Construct bed record from chromsomoe, start location and end location
fromLine :: ByteString -> b Source #
Convert bytestring to bed format
toLine :: b -> ByteString Source #
Convert bed to bytestring
Instances
| BEDConvert BEDGraph Source # | |
| BEDConvert BED3 Source # | |
| BEDConvert BED Source # | |
| BEDConvert NarrowPeak Source # | |
Defined in Bio.Data.Bed.Types Methods asBed :: ByteString -> Int -> Int -> NarrowPeak Source # fromLine :: ByteString -> NarrowPeak Source # toLine :: NarrowPeak -> ByteString Source # convert :: BEDLike b' => b' -> NarrowPeak Source # | |
| BEDConvert BroadPeak Source # | |
| (Read a, Show a, BEDConvert bed) => BEDConvert (BEDExt bed a) Source # | |
BED6 format, as described in http://genome.ucsc.edu/FAQ/FAQformat.html#format1.7
Constructors
| BED | |
Fields
| |
Instances
BED3 format
Constructors
| BED3 | |
Fields | |
Instances
| Eq BED3 Source # | |
| Ord BED3 Source # | |
| Read BED3 Source # | |
| Show BED3 Source # | |
| Generic BED3 Source # | |
| NFData BED3 Source # | |
Defined in Bio.Data.Bed.Types | |
| BEDConvert BED3 Source # | |
| BEDLike BED3 Source # | |
Defined in Bio.Data.Bed.Types | |
| type Rep BED3 Source # | |
Defined in Bio.Data.Bed.Types type Rep BED3 = D1 ('MetaData "BED3" "Bio.Data.Bed.Types" "bioinformatics-toolkit-0.10.0-A8Y5r7ZpZ9gGDfktm9e6ZK" 'False) (C1 ('MetaCons "BED3" 'PrefixI 'True) (S1 ('MetaSel ('Just "_bed3_chrom") 'NoSourceUnpackedness 'NoSourceStrictness 'DecidedStrict) (Rec0 ByteString) :*: (S1 ('MetaSel ('Just "_bed3_chrom_start") 'NoSourceUnpackedness 'NoSourceStrictness 'DecidedStrict) (Rec0 Int) :*: S1 ('MetaSel ('Just "_bed3_chrom_end") 'NoSourceUnpackedness 'NoSourceStrictness 'DecidedStrict) (Rec0 Int)))) | |
Bedgraph format.
Constructors
| BEDGraph | |
Fields
| |
Instances
| Eq BEDGraph Source # | |
| Ord BEDGraph Source # | |
Defined in Bio.Data.Bed.Types | |
| Read BEDGraph Source # | |
| Show BEDGraph Source # | |
| Generic BEDGraph Source # | |
| NFData BEDGraph Source # | |
Defined in Bio.Data.Bed.Types | |
| BEDConvert BEDGraph Source # | |
| BEDLike BEDGraph Source # | |
Defined in Bio.Data.Bed.Types | |
| type Rep BEDGraph Source # | |
Defined in Bio.Data.Bed.Types type Rep BEDGraph = D1 ('MetaData "BEDGraph" "Bio.Data.Bed.Types" "bioinformatics-toolkit-0.10.0-A8Y5r7ZpZ9gGDfktm9e6ZK" 'False) (C1 ('MetaCons "BEDGraph" 'PrefixI 'True) ((S1 ('MetaSel ('Just "_bdg_chrom") 'NoSourceUnpackedness 'NoSourceStrictness 'DecidedStrict) (Rec0 ByteString) :*: S1 ('MetaSel ('Just "_bdg_chrom_start") 'NoSourceUnpackedness 'NoSourceStrictness 'DecidedStrict) (Rec0 Int)) :*: (S1 ('MetaSel ('Just "_bdg_chrom_end") 'NoSourceUnpackedness 'NoSourceStrictness 'DecidedStrict) (Rec0 Int) :*: S1 ('MetaSel ('Just "_bdg_value") 'NoSourceUnpackedness 'NoSourceStrictness 'DecidedStrict) (Rec0 Double)))) | |
data NarrowPeak Source #
ENCODE narrowPeak format: https://genome.ucsc.edu/FAQ/FAQformat.html#format12
Constructors
| NarrowPeak | |
Instances
ENCODE broadPeak format: https://genome.ucsc.edu/FAQ/FAQformat.html#format13
Constructors
| BroadPeak | |
Instances
Instances
type BEDTree a = HashMap ByteString (IntervalMap Int a) Source #