export.cpp File Reference

#include <string>
#include <RcppArmadillo.h>
#include <RcppEigen.h>
#include "GenomicDataStream.h"

Macros
#define	ARMA_WARN_LEVEL   1
#define	MIN(a, b)

Functions
DataFrame	toDF (const VariantInfo *vInfo)
SEXP	create_xptr (const std::string &file, const std::string &field="", const std::string &region="", const std::string &samples="-", const double &MAF=0, const double &minVariance=0, const int &chunkSize=10000, const bool &missingToMean=true)
List	getInfo (SEXP x)
SEXP	setRegions_rcpp (SEXP x, const string &regionString)
SEXP	setChunkSize_rcpp (SEXP x, const double &chunkSize)
CharacterVector	getSampleNames_rcpp (SEXP x)
bool	atEndOfStream_rcpp (SEXP x)
long	featuresRead_rcpp (SEXP x)
DataFrame	getChromRanges_rcpp (SEXP x)
List	getNextChunk_rcpp (SEXP x)
List	summarizeChunks (const shared_ptr< GenomicDataStream > gds, const int &threads=4)
List	summarizeChunks_rcpp (SEXP x, const int &threads=4)
arma::vec	colSums_test (const arma::mat &X)
void	standardize_in_place (arma::mat &X, const bool &center=true, const bool &scale=true)
void	test_DataTable (const string &file, const string &headerKey, const string &delim="\t ")
List	stream_pcaone (SEXP x, const string &region, int m, int k, int nchunks, int s=20, int p=7, int B=64, int threads=4, int threads_eigen=4, const bool verbose=true, const bool scaleAndCenter=true)
Rcpp::List	stream_pcaone_robj (const RObject &x, const std::vector< std::string > &ids, const int &n, const int &chunkSize, const int &nchunks, int m, int k, int s=20, int p=7, int B=64, int threads=4, int threads_eigen=1, const bool verbose=true, const bool scaleAndCenter=true)

Macro Definition Documentation

ARMA_WARN_LEVEL

#define ARMA_WARN_LEVEL   1

MIN

#define MIN	(		a,
			b )

Value:

((a) < (b) ? (a) : (b))

Function Documentation

atEndOfStream_rcpp()

bool atEndOfStream_rcpp

(

SEXP

x

)

colSums_test()

arma::vec colSums_test

(

const arma::mat &

X

)

create_xptr()

SEXP create_xptr	(	const std::string &	file,
		const std::string &	field = "",
		const std::string &	region = "",
		const std::string &	samples = "-",
		const double &	MAF = 0,
		const double &	minVariance = 0,
		const int &	chunkSize = 10000,
		const bool &	missingToMean = true )

featuresRead_rcpp()

long featuresRead_rcpp

(

SEXP

x

)

getChromRanges_rcpp()

DataFrame getChromRanges_rcpp

(

SEXP

x

)

getInfo()

List getInfo

(

SEXP

x

)

getNextChunk_rcpp()

List getNextChunk_rcpp

(

SEXP

x

)

getSampleNames_rcpp()

CharacterVector getSampleNames_rcpp

(

SEXP

x

)

setChunkSize_rcpp()

SEXP setChunkSize_rcpp	(	SEXP	x,
		const double &	chunkSize )

setRegions_rcpp()

SEXP setRegions_rcpp	(	SEXP	x,
		const string &	regionString )

standardize_in_place()

void standardize_in_place	(	arma::mat &	X,
		const bool &	center = true,
		const bool &	scale = true )

stream_pcaone()

List stream_pcaone	(	SEXP	x,
		const string &	region,
		int	m,
		int	k,
		int	nchunks,
		int	s = 20,
		int	p = 7,
		int	B = 64,
		int	threads = 4,
		int	threads_eigen = 4,
		const bool	verbose = true,
		const bool	scaleAndCenter = true )

stream_pcaone_robj()

Rcpp::List stream_pcaone_robj	(	const RObject &	x,
		const std::vector< std::string > &	ids,
		const int &	n,
		const int &	chunkSize,
		const int &	nchunks,
		int	m,
		int	k,
		int	s = 20,
		int	p = 7,
		int	B = 64,
		int	threads = 4,
		int	threads_eigen = 1,
		const bool	verbose = true,
		const bool	scaleAndCenter = true )

summarizeChunks()

List summarizeChunks	(	const shared_ptr< GenomicDataStream >	gds,
		const int &	threads = 4 )

summarizeChunks_rcpp()

List summarizeChunks_rcpp	(	SEXP	x,
		const int &	threads = 4 )

test_DataTable()

void test_DataTable	(	const string &	file,
		const string &	headerKey,
		const string &	delim = "\t " )

toDF()

DataFrame toDF

(

const VariantInfo *

vInfo

)