Writes scTransform-corrected counts to a new store

Reverses the residual transform with every latent variable, the library size included, held at its median, so the depth structure is removed while the per-sample intercept is kept. The result is written as a new gene-major store.

The output is re-indexed: its gene axis is the model's, so gene j in the written store is genes[j + 1] of the source. It also has no normalised layer, since corrected counts carry no library size to scale to.

Usage

rs_sct_corrected_counts(
  f_path_gene,
  residual_fit,
  cell_indices,
  f_path_out,
  gene_batch_size,
  verbose
)

Arguments

f_path_gene

String. Path to the counts_genes.bin file.

residual_fit

List. A scTransform fit from rs_sc_fit_residuals(). The analytic Pearson model has no corrected-count equivalent.

cell_indices

Integer vector. The cell indices to use. (0-indexed!) Must be the selection the fit was fitted on.

f_path_out

String. Path of the gene-major file to write.

gene_batch_size

Integer or NULL. Genes held in memory per batch.

verbose

Integer. 0L - quiet; 1L - normal verbosity; 2L - detailed verbosity.

Value

A list with the following items

• f_path - The file that was written.

• genes - The source gene indices of the written axis. (0-indexed!)

• n_genes - Number of genes written.

• n_cells - Number of cells written.