sparseToDenseMatrix: Convert a sparse matrix to a dense matrix in a block-wise...

In biobenkj/compartmap: Higher-order chromatin domain inference in single samples from methylation arrays and single cells from scRNA-seq and scATAC-seq

Convert a sparse matrix to a dense matrix in a block-wise fashion

Description

Convert a sparse matrix to a dense matrix in a block-wise fashion

Usage

sparseToDenseMatrix(
  mat,
  blockwise = TRUE,
  by.row = TRUE,
  by.col = FALSE,
  chunk.size = 1e+05,
  parallel = FALSE,
  cores = 2
)

Arguments

mat	Input sparse matrix
blockwise	Whether to do the coercion in a block-wise manner
by.row	Whether to chunk in a row-wise fashion
by.col	Whether to chunk in a column-wise fashion
chunk.size	The size of the chunks to use for coercion
parallel	Whether to perform the coercion in parallel
cores	The number of cores to use in the parallel coercion

Value

A dense matrix of the same dimensions as the input

Examples

#make a sparse binary matrix
library(Matrix)
m <- 100
n <- 1000
mat <- round(matrix(runif(m*n), m, n))
mat.sparse <- Matrix(mat, sparse = TRUE)

#coerce back
mat.dense <- sparseToDenseMatrix(mat.sparse, chunk.size = 10)

#make sure they are the same dimensions
dim(mat) == dim(mat.dense)

#make sure they are the same numerically
all(mat == mat.dense)

biobenkj/compartmap documentation built on Oct. 18, 2023, 11:11 a.m.