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GenomicDataStream
A scalable interface between data and analysis
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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 ®ion="", 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 ®ionString) |
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 ¢er=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 ®ion, 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) |
#define ARMA_WARN_LEVEL 1 |
#define MIN | ( | a, | |
b ) |
bool atEndOfStream_rcpp | ( | SEXP | x | ) |
arma::vec colSums_test | ( | const arma::mat & | X | ) |
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 ) |
long featuresRead_rcpp | ( | SEXP | x | ) |
DataFrame getChromRanges_rcpp | ( | SEXP | x | ) |
List getInfo | ( | SEXP | x | ) |
List getNextChunk_rcpp | ( | SEXP | x | ) |
CharacterVector getSampleNames_rcpp | ( | SEXP | x | ) |
SEXP setChunkSize_rcpp | ( | SEXP | x, |
const double & | chunkSize ) |
SEXP setRegions_rcpp | ( | SEXP | x, |
const string & | regionString ) |
void standardize_in_place | ( | arma::mat & | X, |
const bool & | center = true, | ||
const bool & | scale = true ) |
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 ) |
List summarizeChunks | ( | const shared_ptr< GenomicDataStream > | gds, |
const int & | threads = 4 ) |
List summarizeChunks_rcpp | ( | SEXP | x, |
const int & | threads = 4 ) |
void test_DataTable | ( | const string & | file, |
const string & | headerKey, | ||
const string & | delim = "\t " ) |
DataFrame toDF | ( | const VariantInfo * | vInfo | ) |