| Safe Haskell | None |
|---|---|
| Language | Haskell2010 |
SequenceFormats.Plink
Synopsis
- readBimStdIn :: forall (m :: Type -> Type). (MonadThrow m, MonadIO m) => Producer EigenstratSnpEntry m ()
- readBimFile :: forall (m :: Type -> Type). MonadSafe m => FilePath -> Producer EigenstratSnpEntry m ()
- writeBim :: forall (m :: Type -> Type). MonadSafe m => FilePath -> Consumer EigenstratSnpEntry m ()
- readFamFile :: MonadIO m => FilePath -> m [PlinkFamEntry]
- readPlinkBedFile :: MonadSafe m => FilePath -> Int -> m (Producer GenoLine m ())
- readPlink :: MonadSafe m => FilePath -> FilePath -> FilePath -> m ([PlinkFamEntry], Producer (EigenstratSnpEntry, GenoLine) m ())
- writePlink :: forall (m :: Type -> Type). MonadSafe m => FilePath -> FilePath -> FilePath -> [PlinkFamEntry] -> Consumer (EigenstratSnpEntry, GenoLine) m ()
- data PlinkFamEntry = PlinkFamEntry {}
- plinkFam2EigenstratInd :: PlinkPopNameMode -> PlinkFamEntry -> EigenstratIndEntry
- eigenstratInd2PlinkFam :: PlinkPopNameMode -> EigenstratIndEntry -> PlinkFamEntry
- data PlinkPopNameMode
Documentation
readBimStdIn :: forall (m :: Type -> Type). (MonadThrow m, MonadIO m) => Producer EigenstratSnpEntry m () Source #
Function to read a Bim File from StdIn. Returns a Pipes-Producer over the EigenstratSnpEntries.
readBimFile :: forall (m :: Type -> Type). MonadSafe m => FilePath -> Producer EigenstratSnpEntry m () Source #
Function to read a Bim File from a file. Returns a Pipes-Producer over the EigenstratSnpEntries.
Arguments
| :: forall (m :: Type -> Type). MonadSafe m | |
| => FilePath | The Plink Bim File. |
| -> Consumer EigenstratSnpEntry m () | A consumer to read EigenstratSnpEntries |
Function to write a Bim file. Returns a consumer expecting EigenstratSnpEntries.
readFamFile :: MonadIO m => FilePath -> m [PlinkFamEntry] Source #
Function to read a Plink fam file. Returns the Eigenstrat Individual Entries as list.
readPlinkBedFile :: MonadSafe m => FilePath -> Int -> m (Producer GenoLine m ()) Source #
A function to read a bed file from a file. Returns a Producer over all lines.
Arguments
| :: MonadSafe m | |
| => FilePath | The Bed file |
| -> FilePath | The Bim File |
| -> FilePath | The Fam file |
| -> m ([PlinkFamEntry], Producer (EigenstratSnpEntry, GenoLine) m ()) |
Function to read a full Plink dataset from files. Returns a pair of the Plink Individual Entries, and a joint Producer over the snp entries and the genotypes.
Arguments
| :: forall (m :: Type -> Type). MonadSafe m | |
| => FilePath | The Bed file |
| -> FilePath | The Bim File |
| -> FilePath | The Fam file |
| -> [PlinkFamEntry] | The list of individual entries |
| -> Consumer (EigenstratSnpEntry, GenoLine) m () | A consumer to read joint Snp/Genotype entries. |
Function to write a Plink Database. Returns a consumer expecting joint Snp- and Genotype lines.
data PlinkFamEntry Source #
Constructors
| PlinkFamEntry | |
Fields | |
Instances
| Show PlinkFamEntry Source # | |
Defined in SequenceFormats.Plink Methods showsPrec :: Int -> PlinkFamEntry -> ShowS # show :: PlinkFamEntry -> String # showList :: [PlinkFamEntry] -> ShowS # | |
| Eq PlinkFamEntry Source # | |
Defined in SequenceFormats.Plink Methods (==) :: PlinkFamEntry -> PlinkFamEntry -> Bool # (/=) :: PlinkFamEntry -> PlinkFamEntry -> Bool # | |
data PlinkPopNameMode Source #
Instances
| Show PlinkPopNameMode Source # | |
Defined in SequenceFormats.Plink Methods showsPrec :: Int -> PlinkPopNameMode -> ShowS # show :: PlinkPopNameMode -> String # showList :: [PlinkPopNameMode] -> ShowS # | |
| Eq PlinkPopNameMode Source # | |
Defined in SequenceFormats.Plink Methods (==) :: PlinkPopNameMode -> PlinkPopNameMode -> Bool # (/=) :: PlinkPopNameMode -> PlinkPopNameMode -> Bool # | |