Helper function to write data to a cell ranger like output

This is a helper to write synthetic data to cell ranger like output, i.e., an .mtx file, an barcodes.csv (or .tsv) and a features.csv (or .tsv).

Usage

write_cellranger_output(
  f_path,
  counts,
  obs,
  var,
  format_type = c("csv", "tsv"),
  rows = c("cells", "genes"),
  overwrite = TRUE,
  .verbose = TRUE
)

Arguments

f_path

String. The filepath to which to save the data

counts

Sparse matrix. Needs to be of class dgRMatrix or dgCMatrix.

obs

data.table. The observations. Needs to have nrow(obs) == nrow(counts).

var

data.table. The variable data. Needs to have ncol(var) == ncol(counts).

format_type

String. One of c("csv", "tsv"). Shall the data be saved in TSV or CSV.

rows

String. One of c("cells", "genes"). Shall the rows represent cells or genes in the .mtx file.

overwrite

Boolean. Shall any found h5ad file be overwritten.

.verbose

Boolean. Controls verbosity of the function.

Value

Returns invisible

Examples

# the 10x trio: an .mtx plus barcode and feature tables
data <- generate_single_cell_test_data(
  syn_data_params = params_sc_synthetic_data(n_cells = 200L, n_genes = 40L)
)
dir_out <- tempfile("cellranger")
dir.create(dir_out, recursive = TRUE)
write_cellranger_output(
  f_path = dir_out,
  counts = data$counts,
  obs = data$obs,
  var = data$var,
  rows = "cells",
  format_type = "csv",
  .verbose = FALSE
)
list.files(dir_out)
#> [1] "barcodes.csv" "features.csv" "matrix.mtx"  

unlink(dir_out, recursive = TRUE, force = TRUE)