Safe Haskell	Safe-Inferred
Language	Haskell2010

SequenceFormats.Plink

Synopsis

readBimStdIn :: (MonadThrow m, MonadIO m) => Producer EigenstratSnpEntry m ()
readBimFile :: MonadSafe m => FilePath -> Producer EigenstratSnpEntry m ()
writeBim :: MonadIO m => Handle -> 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 :: MonadSafe m => FilePath -> FilePath -> FilePath -> [PlinkFamEntry] -> Consumer (EigenstratSnpEntry, GenoLine) m ()
data PlinkFamEntry = PlinkFamEntry {
- _famFamilyID :: String
- _famIndividualID :: String
- _famFatherID :: String
- _famMotherID :: String
- _famSexCode :: Sex
- _famPhenotype :: String
}
plinkFam2EigenstratInd :: PlinkPopNameMode -> PlinkFamEntry -> EigenstratIndEntry
eigenstratInd2PlinkFam :: PlinkPopNameMode -> EigenstratIndEntry -> PlinkFamEntry
data PlinkPopNameMode

Documentation

readBimStdIn :: (MonadThrow m, MonadIO m) => Producer EigenstratSnpEntry m () Source #

Function to read a Bim File from StdIn. Returns a Pipes-Producer over the EigenstratSnpEntries.

readBimFile :: MonadSafe m => FilePath -> Producer EigenstratSnpEntry m () Source #

Function to read a Bim File from a file. Returns a Pipes-Producer over the EigenstratSnpEntries.

writeBim Source #

Arguments

:: MonadIO m
=> Handle	The Eigenstrat Snp File handle.
-> 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.

readPlink Source #

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.

writePlink Source #

Arguments

:: 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 _famFamilyID :: String _famIndividualID :: String _famFatherID :: String _famMotherID :: String _famSexCode :: Sex _famPhenotype :: String

Instances

Instances details

Show PlinkFamEntry Source #
Instance details Defined in SequenceFormats.Plink Methods showsPrec :: Int -> PlinkFamEntry -> ShowS # show :: PlinkFamEntry -> String # showList :: [PlinkFamEntry] -> ShowS #
Eq PlinkFamEntry Source #
Instance details Defined in SequenceFormats.Plink Methods (==) :: PlinkFamEntry -> PlinkFamEntry -> Bool # (/=) :: PlinkFamEntry -> PlinkFamEntry -> Bool #

plinkFam2EigenstratInd :: PlinkPopNameMode -> PlinkFamEntry -> EigenstratIndEntry Source #

eigenstratInd2PlinkFam :: PlinkPopNameMode -> EigenstratIndEntry -> PlinkFamEntry Source #

data PlinkPopNameMode Source #

Constructors

PlinkPopNameAsFamily
PlinkPopNameAsPhenotype
PlinkPopNameAsBoth

Instances

Instances details

Show PlinkPopNameMode Source #
Instance details Defined in SequenceFormats.Plink Methods showsPrec :: Int -> PlinkPopNameMode -> ShowS # show :: PlinkPopNameMode -> String # showList :: [PlinkPopNameMode] -> ShowS #
Eq PlinkPopNameMode Source #
Instance details Defined in SequenceFormats.Plink Methods (==) :: PlinkPopNameMode -> PlinkPopNameMode -> Bool # (/=) :: PlinkPopNameMode -> PlinkPopNameMode -> Bool #