run_dtw: Get network adjacency dataframe based on DTW method

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

Get network adjacency dataframe based on DTW method

Description

Use DTW to calcuate gene-gene distance based on their expression and pseudotime

Usage

run_dtw(
  expression_matrix,
  pseudotime_list,
  slide_window_size = 50,
  slide_step_size = 25,
  quantile_cutoff = 5,
  cores = 1
)

Arguments

expression_matrix	expression matrix data
pseudotime_list	list of pseudotime
slide_window_size	sliding window size
slide_step_size	sliding window step size
quantile_cutoff	an integer value (1-99) for quantile cutoff
cores	number of cores for parallel computing

Value

adjacency dataframe (with columns "from, to, distance,direction, similarity")

Examples

example_data <- pGRNDB
expression_matrix <- example_data[["expression"]]
pseudotime_list <- example_data[["ptime"]]$PseudoTime
adj_df <- run_dtw(expression_matrix,
                  pseudotime_list,
                  quantile_cutoff=50,
                  cores=1)
                  

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