# Run gRNA-gene pair analysis at scale

`run_gRNA_gene_pair_analysis_at_scale.Rd`

Runs the gene-gRRNA pair ananysis across an entire pod of gene-gRNA pairs.

    run_gRNA_gene_pair_analysis_at_scale(
      pod_id,
      gene_precomp_dir,
      gRNA_precomp_dir,
      results_dir,
      log_dir,
      gene_matrix,
      combined_perturbation_matrix,
      covariate_matrix,
      regularization_amount,
      side,
      B,
      full_output
    )

## Arguments

pod_id

  id of the pod to compute

gene_precomp_dir

  the directory containing the results of the gene precomputation

gRNA_precomp_dir

  the directory containing the results of the gRNA precomputation

results_dir

  directory in which to store the results

log_dir

  (optional) directory in which to sink the log file

gene_matrix

  a gene-by-cell expression matrix; the rows (i.e., gene IDs) and columns (i.e., cell barcodes) should be named

combined_perturbation_matrix

  a binary matrix of perturbations (i.e., gRNA group-to-cell assignments); the rows (i.e., gRNA groups) and columns (i.e., cell barcodes) should be named.

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

side

  sidedness of the test; one of "both," "left," and "right"

B

  number of resamples to draw for the conditional randomization test

full_output

  return the full output (TRUE) or a simplified, reduced output (FALSE; default)?