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Fits a residual model for single cell data

rs_sc_fit_residuals.Rd

[Experimental] Fits either scTransform (v2) or the analytic Pearson residual model of Lause, Berens and Kobak over the selected cells. With group_of_cell one model is fitted per group, which is what a multi-sample experiment wants: each sample keeps its own sequencing depth and composition.

The fit is returned as a list rather than applied to anything. Hand it back to rs_sc_residual_variance(), rs_sc_pca_residuals() or rs_sct_corrected_counts() to use it.

Usage

rs_sc_fit_residuals(
  f_path_gene,
  f_path_cell,
  method,
  cell_indices,
  group_of_cell,
  covariates,
  params,
  gene_batch_size,
  seed,
  verbose
)

Arguments

f_path_gene

String. Path to the counts_genes.bin file.

f_path_cell

String. Path to the counts_cells.bin file. Used for the library sizes, and for the per-cell totals of the analytic Pearson fit.

method

String. One of c("sctransform", "analytic_pearson").

cell_indices

Integer vector. The cell indices to use. (0-indexed!)

group_of_cell

Integer vector or NULL. Group label per selected cell. (0-indexed, dense!) NULL fits one model over every cell.

covariates

Named list of numeric vectors, one per covariate, each of length length(cell_indices). scTransform only. The order is remembered and checked on every subsequent use.

params

Named list. The parameters, see params_sc_sctransform() or params_sc_apr().

gene_batch_size

Integer or NULL. Genes held in memory per batch.

seed

Integer. Seed for the step-1 subsample.

verbose

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

Value

A list with the following items

  • method - The method that was fitted.

  • models - The per-group models.

  • genes - The gene indices modelled in every group. (0-indexed!)

  • group_of_cell - The group label per selected cell. (0-indexed!)

  • n_groups - Number of groups.

  • cell_indices - The cells that were fitted on. (0-indexed!)

  • covariates - The covariates used, scTransform only.

  • log10_umi - The per-cell offset, scTransform only.

  • cell_totals - The per-cell totals, analytic Pearson only.

References

Choudhary and Satija, Genome Biology, 2022; Lause, Berens and Kobak, Genome Biology, 2021.