matrix2adj: Convert distance matrix to adjacency dataframe

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

Convert distance matrix to adjacency dataframe

Description

Convert distance matrix to adjacency dataframe for network construction.

Usage

matrix2adj(data, quantile_cutoff = 5)

Arguments

data	distance matrix
quantile_cutoff	an integer value (1-99) for quantile cutoff

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
dtw_dist_matrix <- get_dtw_dist_mat(expression_matrix,
                                    pseudotime_list,
                                    cores=1)
adj_df <- matrix2adj(dtw_dist_matrix)

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