Run sceptre on a gRNA-gene pair

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")
}