Run gene precomputation at scale round 2

Runs the second round of gene precomputations.

run_gene_precomputation_at_scale_round_2(
  pod_id,
  gene_precomp_dir,
  gene_matrix,
  covariate_matrix,
  regularization_amount,
  log_dir
)

Arguments

pod_id

pod id

gene_precomp_dir

gene precomp dir

gene_matrix

the gene expression matrix, stored as an ondisc_matrix

covariate_matrix

the cell-specific matrix of technical factors, ideally containing the following covariates: log-transformed gene library size (numeric), log-transformed gRNA library size (numeric), percent mitochondrial reads (numeric), and batch (factor). The rows (i.e., cell barcodes) should be named

regularization_amount

non-negative number specifying the amount of regularization to apply to the negative binomial dispersion parameter estimates

log_dir

directory in which to sink the logs