Big Memory Package matrix reference wrap

big_memory.R

library('bigmemory')
options(bigmemory.allow.dimnames = TRUE)

# Read SingleCellExperiment object
sce <- readRDS('lake.rds')
normcounts(sce) <- as.big.matrix(normcounts(sce)) 

process(normcounts(sce))

process.cpp

// [[Rcpp::depends(BH, bigmemory)]]
#include <Rcpp.h>
#include <RcppArmadillo.h>
#include <bigmemory/MatrixAccessor.hpp>
#include <bigmemory/BigMatrix.h>

arma::mat cast_big_matrix(const SEXP& mat)
{
   Rcpp::XPtr<BigMatrix> xpMat(mat);
   return arma::mat((double*)xpMat->matrix(), xpMat->nrow(), xpMat->ncol(), false);
}


arma::mat process(const SEXP& mat)
{
  arma::mat matrix(cast_big_matrix(mat));
  // Do processing
  return matrix;
}

Pros

• Works with large matrices that can not fit in memory

Cons

• Have to cast matrix to big matrix at least once.
• We loose regular R matrix functionality:

   > t<- sce@assays$data$normcounts 
   > t <- as.big.matrix(t) 
   > t == 0
   Error in t == 0 : 
   comparison (1) is possible only for atomic and list types