Helper to generate cell ranger input parameters

Resolves the three files a Cell Ranger MTX directory holds and wraps them into the parameter list load_mtx() wants. Handles the v2 naming (genes.tsv) and the v3 one (features.tsv), and the .csv variant that write_cellranger_output() can emit.

Usage

get_cell_ranger_params(dir_data, cells_as_rows = FALSE, has_hdr = FALSE)

Arguments

dir_data

String. The directory with the Cell Ranger outputs

cells_as_rows

Boolean. Are the cells the rows of the matrix? Cell Ranger writes genes x cells, so this defaults to FALSE. Set to TRUE for output of write_cellranger_output() written with rows = "cells".

has_hdr

Boolean. Do the barcode and feature files carry a header row? Cell Ranger writes none, so this defaults to FALSE. write_cellranger_output() does write one.

Value

A list based on params_sc_mtx_io().

Examples

# round trip through the package's own writer
dir <- tempfile("cellranger")
dir.create(dir)
data <- generate_single_cell_test_data(
  syn_data_params = params_sc_synthetic_data(n_cells = 50L, n_genes = 40L)
)
write_cellranger_output(
  f_path = dir,
  counts = data$counts,
  obs = data$obs,
  var = data$var,
  rows = "genes",
  format_type = "tsv",
  .verbose = FALSE
)
str(get_cell_ranger_params(dir, has_hdr = TRUE))
#> List of 5
#>  $ path_mtx     : chr "/tmp/RtmpvYy6aB/cellranger47b12f5fe1ba/matrix.mtx"
#>  $ path_obs     : chr "/tmp/RtmpvYy6aB/cellranger47b12f5fe1ba/barcodes.tsv"
#>  $ path_var     : chr "/tmp/RtmpvYy6aB/cellranger47b12f5fe1ba/features.tsv"
#>  $ cells_as_rows: logi FALSE
#>  $ has_hdr      : logi TRUE

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