# Run gene precomputation at scale round 2

`run_gene_precomputation_at_scale_round_2.Rd`

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