| Safe Haskell | Safe-Inferred |
|---|---|
| Language | Haskell2010 |
Poseidon.GenotypeData
Synopsis
- data GenoDataSource
- = PacBaseDir { }
- | GenoDirect { }
- data GenotypeDataSpec = GenotypeDataSpec {}
- data GenotypeFormatSpec
- data SNPSetSpec
- snpSetMergeList :: [SNPSetSpec] -> Bool -> SNPSetSpec
- snpSetMerge :: SNPSetSpec -> SNPSetSpec -> Bool -> SNPSetSpec
- loadIndividuals :: FilePath -> GenotypeDataSpec -> PoseidonIO [EigenstratIndEntry]
- loadGenotypeData :: MonadSafe m => FilePath -> GenotypeDataSpec -> PlinkPopNameMode -> m ([EigenstratIndEntry], Producer (EigenstratSnpEntry, GenoLine) m ())
- joinEntries :: MonadIO m => LogA -> [Int] -> [String] -> [Maybe (EigenstratSnpEntry, GenoLine)] -> m (EigenstratSnpEntry, GenoLine)
- getConsensusSnpEntry :: MonadIO m => LogA -> [EigenstratSnpEntry] -> m EigenstratSnpEntry
- recodeAlleles :: EigenstratSnpEntry -> EigenstratSnpEntry -> GenoLine -> Either String GenoLine
- printSNPCopyProgress :: MonadIO m => LogA -> UTCTime -> Pipe a a m ()
- selectIndices :: [Int] -> (EigenstratSnpEntry, GenoLine) -> (EigenstratSnpEntry, GenoLine)
Documentation
data GenoDataSource Source #
Constructors
| PacBaseDir | |
Fields | |
| GenoDirect | |
Fields | |
Instances
| Show GenoDataSource Source # | |
Defined in Poseidon.GenotypeData Methods showsPrec :: Int -> GenoDataSource -> ShowS # show :: GenoDataSource -> String # showList :: [GenoDataSource] -> ShowS # | |
data GenotypeDataSpec Source #
A datatype to specify genotype files
Constructors
| GenotypeDataSpec | |
Fields
| |
Instances
| FromJSON GenotypeDataSpec Source # | To facilitate automatic parsing of GenotypeDataSpec from JSON files |
Defined in Poseidon.GenotypeData Methods parseJSON :: Value -> Parser GenotypeDataSpec parseJSONList :: Value -> Parser [GenotypeDataSpec] | |
| ToJSON GenotypeDataSpec Source # | |
Defined in Poseidon.GenotypeData Methods toJSON :: GenotypeDataSpec -> Value toEncoding :: GenotypeDataSpec -> Encoding toJSONList :: [GenotypeDataSpec] -> Value toEncodingList :: [GenotypeDataSpec] -> Encoding | |
| Show GenotypeDataSpec Source # | |
Defined in Poseidon.GenotypeData Methods showsPrec :: Int -> GenotypeDataSpec -> ShowS # show :: GenotypeDataSpec -> String # showList :: [GenotypeDataSpec] -> ShowS # | |
| Eq GenotypeDataSpec Source # | |
Defined in Poseidon.GenotypeData Methods (==) :: GenotypeDataSpec -> GenotypeDataSpec -> Bool # (/=) :: GenotypeDataSpec -> GenotypeDataSpec -> Bool # | |
data GenotypeFormatSpec Source #
A data type representing the options fo the genotype format
Constructors
| GenotypeFormatEigenstrat | |
| GenotypeFormatPlink |
Instances
| FromJSON GenotypeFormatSpec Source # | To facilitate automatic parsing of GenotypeFormatSpec from JSON files |
Defined in Poseidon.GenotypeData Methods parseJSON :: Value -> Parser GenotypeFormatSpec parseJSONList :: Value -> Parser [GenotypeFormatSpec] | |
| ToJSON GenotypeFormatSpec Source # | |
Defined in Poseidon.GenotypeData Methods toJSON :: GenotypeFormatSpec -> Value toEncoding :: GenotypeFormatSpec -> Encoding toJSONList :: [GenotypeFormatSpec] -> Value toEncodingList :: [GenotypeFormatSpec] -> Encoding | |
| Show GenotypeFormatSpec Source # | |
Defined in Poseidon.GenotypeData Methods showsPrec :: Int -> GenotypeFormatSpec -> ShowS # show :: GenotypeFormatSpec -> String # showList :: [GenotypeFormatSpec] -> ShowS # | |
| Eq GenotypeFormatSpec Source # | |
Defined in Poseidon.GenotypeData Methods (==) :: GenotypeFormatSpec -> GenotypeFormatSpec -> Bool # (/=) :: GenotypeFormatSpec -> GenotypeFormatSpec -> Bool # | |
data SNPSetSpec Source #
Constructors
| SNPSet1240K | |
| SNPSetHumanOrigins | |
| SNPSetOther |
Instances
| FromJSON SNPSetSpec Source # | |
Defined in Poseidon.GenotypeData | |
| ToJSON SNPSetSpec Source # | |
Defined in Poseidon.GenotypeData Methods toJSON :: SNPSetSpec -> Value toEncoding :: SNPSetSpec -> Encoding toJSONList :: [SNPSetSpec] -> Value toEncodingList :: [SNPSetSpec] -> Encoding | |
| Show SNPSetSpec Source # | |
Defined in Poseidon.GenotypeData Methods showsPrec :: Int -> SNPSetSpec -> ShowS # show :: SNPSetSpec -> String # showList :: [SNPSetSpec] -> ShowS # | |
| Eq SNPSetSpec Source # | |
Defined in Poseidon.GenotypeData | |
snpSetMergeList :: [SNPSetSpec] -> Bool -> SNPSetSpec Source #
snpSetMerge :: SNPSetSpec -> SNPSetSpec -> Bool -> SNPSetSpec Source #
Arguments
| :: FilePath | the base directory |
| -> GenotypeDataSpec | the Genotype spec |
| -> PoseidonIO [EigenstratIndEntry] | the returned list of EigenstratIndEntries. |
A function to return a list of all individuals in the genotype files of a package.
Arguments
| :: MonadSafe m | |
| => FilePath | the base path |
| -> GenotypeDataSpec | the genotype spec |
| -> PlinkPopNameMode | The Plink PopName Mode |
| -> m ([EigenstratIndEntry], Producer (EigenstratSnpEntry, GenoLine) m ()) | a pair of the EigenstratIndEntries and a Producer over the Snp position values and the genotype line. |
A function to read the genotype data of a package
joinEntries :: MonadIO m => LogA -> [Int] -> [String] -> [Maybe (EigenstratSnpEntry, GenoLine)] -> m (EigenstratSnpEntry, GenoLine) Source #
getConsensusSnpEntry :: MonadIO m => LogA -> [EigenstratSnpEntry] -> m EigenstratSnpEntry Source #
recodeAlleles :: EigenstratSnpEntry -> EigenstratSnpEntry -> GenoLine -> Either String GenoLine Source #
selectIndices :: [Int] -> (EigenstratSnpEntry, GenoLine) -> (EigenstratSnpEntry, GenoLine) Source #