run_granger_test: Use Granger-causality Test to get gene-gene regulatory...

In pGRN: Single-Cell RNA Sequencing Pseudo-Time Based Gene Regulatory Network Inference

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)

pGRN documentation built on Jan. 18, 2023, 1:06 a.m.