gds::DelayedStream Class Reference

#include <DelayedStream.h>

Inheritance diagram for gds::DelayedStream:

Public Member Functions
	DelayedStream (const shared_ptr< tatami::NumericMatrix > &ptr, const vector< string > &rowNames, const int &chunkSize)
	~DelayedStream ()
void	setRegions (const vector< string > &regions) override
int	n_samples () override
int	n_rows ()
vector< string >	getSampleNames () override
string	getStreamType () override
GenomicRanges	getChromRanges () override
bool	getNextChunk (DataChunk< arma::mat > &chunk, const bool &useFilter=true) override
bool	getNextChunk (DataChunk< arma::sp_mat > &chunk, const bool &useFilter=true) override
bool	getNextChunk (DataChunk< Eigen::MatrixXd > &chunk, const bool &useFilter=true) override
bool	getNextChunk (DataChunk< Eigen::SparseMatrix< double > > &chunk, const bool &useFilter=true) override
bool	getNextChunk (DataChunk< Rcpp::NumericMatrix > &chunk, const bool &useFilter=true) override
bool	getNextChunk (DataChunk< vector< double > > &chunk, const bool &useFilter=true) override
void	getNextChunk (DataChunk< Eigen::MatrixXd > &chunk, int start, int len)
Public Member Functions inherited from gds::GenomicDataStream
	GenomicDataStream ()
	GenomicDataStream (const Param &param)
virtual	~GenomicDataStream ()
double	getMinVariance ()
double	getMAF () const
void	setMinVariance (const double &value)
void	setChunkSize (const int &chunkSize)
Param	getParam () const

Additional Inherited Members
Protected Attributes inherited from gds::GenomicDataStream
Param	param

Detailed Description

Reads an Robject

Constructor & Destructor Documentation

DelayedStream()

gds::DelayedStream::DelayedStream ( const shared_ptr< tatami::NumericMatrix > & ptr, const vector< string > & rowNames, const int & chunkSize )

inline

~DelayedStream()

gds::DelayedStream::~DelayedStream ( )

inline

destructor

Member Function Documentation

getChromRanges()

GenomicRanges gds::DelayedStream::getChromRanges ( )

inlineoverridevirtual

Get maximum position for each chrom

Implements gds::GenomicDataStream.

getNextChunk() [1/7]

bool gds::DelayedStream::getNextChunk ( DataChunk< arma::mat > & chunk, const bool & useFilter = true )

inlineoverridevirtual

Get next chunk of features as arma::mat

Implements gds::GenomicDataStream.

getNextChunk() [2/7]

bool gds::DelayedStream::getNextChunk ( DataChunk< arma::sp_mat > & chunk, const bool & useFilter = true )

inlineoverridevirtual

Get next chunk of features as arma::sp_mat

Implements gds::GenomicDataStream.

getNextChunk() [3/7]

bool gds::DelayedStream::getNextChunk ( DataChunk< Eigen::MatrixXd > & chunk, const bool & useFilter = true )

inlineoverridevirtual

Get next chunk of features as Eigen::MatrixXd

Implements gds::GenomicDataStream.

getNextChunk() [4/7]

void gds::DelayedStream::getNextChunk ( DataChunk< Eigen::MatrixXd > & chunk, int start, int len )

inline

Get chunks based on start and end

getNextChunk() [5/7]

bool gds::DelayedStream::getNextChunk ( DataChunk< Eigen::SparseMatrix< double > > & chunk, const bool & useFilter = true )

inlineoverridevirtual

Get next chunk of features as SparseMatrix<double>

Implements gds::GenomicDataStream.

getNextChunk() [6/7]

bool gds::DelayedStream::getNextChunk ( DataChunk< Rcpp::NumericMatrix > & chunk, const bool & useFilter = true )

inlineoverridevirtual

Get next chunk of features as Rcpp::NumericMatrix

Implements gds::GenomicDataStream.

getNextChunk() [7/7]

bool gds::DelayedStream::getNextChunk ( DataChunk< vector< double > > & chunk, const bool & useFilter = true )

inlineoverridevirtual

Get next chunk of features as vector<double>

Implements gds::GenomicDataStream.

getSampleNames()

vector< string > gds::DelayedStream::getSampleNames ( )

inlineoverridevirtual

Get vector of sample names in order that the genotypes are extracted

Implements gds::GenomicDataStream.

getStreamType()

string gds::DelayedStream::getStreamType ( )

inlineoverridevirtual

get FileType of param.file

Implements gds::GenomicDataStream.

n_rows()

int gds::DelayedStream::n_rows ( )

inline

Get number of rows in data matrix

n_samples()

int gds::DelayedStream::n_samples ( )

inlineoverridevirtual

Get number of columns in data matrix

Implements gds::GenomicDataStream.

setRegions()

void gds::DelayedStream::setRegions ( const vector< string > & regions )

inlineoverridevirtual

setter

Implements gds::GenomicDataStream.

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The documentation for this class was generated from the following file:

• inst/include/DelayedStream.h