Transpose the storage order for a matrix

Transpose the storage order for a matrix

Usage

transpose_storage_order(
  matrix,
  outdir = tempfile("transpose"),
  tmpdir = tempdir(),
  load_bytes = 4194304L,
  sort_bytes = 1073741824L
)

Arguments

matrix

Input matrix

outdir

Directory to store the output

tmpdir

Temporary directory to use for intermediate storage

load_bytes

The minimum contiguous load size during the merge sort passes

sort_bytes

The amount of memory to allocate for re-sorting chunks of entries

Value

MatrixDir object with a copy of the input matrix, but the storage order flipped

Details

This re-sorts the entries of a matrix to change the storage order from row-major to col-major. For large matrices, this can be slow – around 2 minutes to transpose a 500k cell RNA-seq matrix The default load_bytes (4MiB) and sort_bytes (1GiB) parameters allow ~85GB of data to be sorted with two passes through the data, and ~7.3TB of data to be sorted in three passes through the data.