run_granger_test {pGRN}

Use Granger-causality Test to get gene-gene regulatory relationship

Description

Based on single-cell gene expression matrix and pseudotime, calculate Granger-causality Test based gene-gene regulatory relationship

Usage

run_granger_test(
  data,
  ptime,
  slide_window_size = 20,
  slide_step_size = 10,
  pvalue_cutoff = 0.01,
  order = 1,
  ...
)

Arguments

data

gene expression matrix (Gene * Cells)

ptime

pseudotime matched with the column cells of the gene expression matrix

slide_window_size

sliding window size

slide_step_size

sliding window step size

pvalue_cutoff

cutoff for the pvalue from transfer entropy test

order

integer specifying the order of lags to include in the auxiliary regression

...

other parameters for grangertest function in lmtest

Value

adjacency data frame

Examples

example_data <- pGRNDB
expression_matrix <- example_data[["expression"]]
pseudotime_list <- example_data[["ptime"]]$PseudoTime
gt_adj_df <- run_granger_test(expression_matrix, pseudotime_list)