# Run `sceptre` on a gRNA-gene pair

`run_sceptre_gRNA_gene_pair.Rd`

Runs `sceptre` on a given gRNA-gene pair.

    run_sceptre_gRNA_gene_pair(
      gene_expressions,
      gRNA_expressions,
      covariate_matrix,
      side = "both",
      B = 1500,
      full_output = FALSE,
      seed = 4
    )

## Arguments

gene_expressions

  (numeric vector) a vector of gene expressions

gRNA_expressions

  (numeric vector) a vector of gRNA expressions (or, optionally, a user-thresholded vector of binary gRNA indicators)

covariate_matrix

  (data frame) the cell-specific matrix of covariates

side

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

B

  number of resamples for the conditional randomization test

full_output

  return the full output (TRUE) or a streamlined, reduced output (FALSE)?

seed

  seed to the random number generator

## Details

This function is for demonstration purposes only. The function `run_sceptre_in_memory` should be used when testing for association between multiple genes and gRNAs.

## Examples

    if (FALSE) {
    # load the example data
    data(gene_matrix); data(gRNA_matrix); data(covariate_matrix)
    gene_expressions <- gene_matrix[1,]
    gRNA_expressions <- gRNA_matrix[1,]
    # run method
    result <- run_sceptre_gRNA_gene_pair(gene_expressions, gRNA_expressions, covariate_matrix, "left")
    }