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Write a sparse matrix to a StreamPress file

Source: R/streampress.R
st_write.Rd

Write a sparse matrix to a StreamPress file

Usage

st_write(
  x,
  path,
  obs = NULL,
  var = NULL,
  delta = TRUE,
  value_pred = FALSE,
  verbose = FALSE,
  precision = "auto",
  row_sort = FALSE,
  include_transpose = TRUE,
  chunk_cols = NULL,
  chunk_bytes = 8e+06,
  transp_chunk_cols = NULL,
  transp_chunk_bytes = NULL,
  threads = 0L
)

Arguments

x

A sparse matrix (dgCMatrix) or object coercible to one.

path

Output file path. Extension .spz is recommended.

obs

Optional data.frame of observation (row/cell) metadata. Must have nrow(obs) == nrow(x).

var

Optional data.frame of variable (column/gene) metadata. Must have nrow(var) == ncol(x).

delta

Logical; use density-based delta prediction for structure. Default TRUE.

value_pred

Logical; use value prediction for integer-valued data. Default FALSE.

verbose

Logical; print compression statistics. Default FALSE.

precision

Value precision: "auto" (default), "fp32", "fp16", "quant8", "fp64".

row_sort

Logical; sort rows by nnz for better compression.

include_transpose

Logical; store CSC(A^T) in the file. Default TRUE.

chunk_cols

Integer or NULL; columns per chunk. If NULL, computed from chunk_bytes.

chunk_bytes

Numeric; target bytes per chunk when chunk_cols is NULL. Default 8 MB, which yields ~50 columns per chunk for typical scRNA-seq matrices (~38 k rows). Smaller chunks create more parallel work during reading; larger chunks compress slightly better.

transp_chunk_cols

Integer or NULL; columns per transpose chunk.

transp_chunk_bytes

Numeric or NULL; target bytes per transpose chunk.

threads

Integer; number of threads for parallel compression (0 = all available). Default 0.

Value

Invisibly returns a list with compression statistics.

See also

st_read, st_info

Examples

# \donttest{
library(Matrix)
A <- rsparsematrix(1000, 500, 0.05)
f <- tempfile(fileext = ".spz")
st_write(A, f)
B <- st_read(f)
all.equal(A, B)  # TRUE
#> [1] "Mean relative difference: 2.431235e-08"
unlink(f)
# }