GenomicDataStream
A scalable interface between data and analysis
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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)