get_dtw_dist_mat: DTW distance matrix for all genes

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

DTW distance matrix for all genes

Description

Get DTW distance matrix for all genes using pseudotime based sliding window transfromation, parallel computing allowed.

Usage

get_dtw_dist_mat(
  data,
  ptime,
  slide_window_size = 50,
  slide_step_size = 25,
  cores = 2
)

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
cores	number of cores for parallel computing

Value

bidirectional DTW distance matrix

Examples

example_data <- pGRNDB
expression_matrix <- example_data[["expression"]]
pseudotime_list <- example_data[["ptime"]]$PseudoTime
dtw_dist_matrix <- get_dtw_dist_mat(expression_matrix,
                                    pseudotime_list,
                                    cores=1)

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