Safe Haskell | None |
---|---|
Language | Haskell2010 |
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 {
- _bed_chrom :: !ByteString
- _bed_chromStart :: !Int
- _bed_chromEnd :: !Int
- _bed_name :: !(Maybe ByteString)
- _bed_score :: !(Maybe Int)
- _bed_strand :: !(Maybe Bool)
- data BED3 = BED3 {
- _bed3_chrom :: !ByteString
- _bed3_chrom_start :: !Int
- _bed3_chrom_end :: !Int
- 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).
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 NarrowPeak Source # | |
Defined in Bio.Data.Bed.Types 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 BED3 Source # | |
BEDLike BED Source # | |
BEDLike BroadPeak Source # | |
BEDLike bed => BEDLike (BEDExt bed a) Source # | |
Defined in Bio.Data.Bed.Types |
class BEDLike b => BEDConvert b where Source #
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 NarrowPeak Source # | |
Defined in Bio.Data.Bed.Types asBed :: ByteString -> Int -> Int -> NarrowPeak Source # fromLine :: ByteString -> NarrowPeak Source # toLine :: NarrowPeak -> ByteString Source # convert :: BEDLike b' => b' -> NarrowPeak Source # | |
BEDConvert BED3 Source # | |
BEDConvert BED Source # | |
BEDConvert BroadPeak Source # | |
(Default a, 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
BED | |
|
BED3 | |
|
data NarrowPeak Source #
ENCODE narrowPeak format: https://genome.ucsc.edu/FAQ/FAQformat.html#format12
Instances
ENCODE broadPeak format: https://genome.ucsc.edu/FAQ/FAQformat.html#format13
Instances
Eq BroadPeak Source # | |
Read BroadPeak Source # | |
Show BroadPeak Source # | |
BEDConvert BroadPeak Source # | |
BEDLike BroadPeak Source # | |
Instances
(Eq bed, Eq a) => Eq (BEDExt bed a) Source # | |
(Read bed, Read a) => Read (BEDExt bed a) Source # | |
(Show bed, Show a) => Show (BEDExt bed a) Source # | |
(Default a, Read a, Show a, BEDConvert bed) => BEDConvert (BEDExt bed a) Source # | |
BEDLike bed => BEDLike (BEDExt bed a) Source # | |
Defined in Bio.Data.Bed.Types |
type BEDTree a = HashMap ByteString (IntervalMap Int a) Source #