pGRN: scRNA-Seq Pseudotime Based Gene Regulatory Netowrk Inference

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

knitr::opts_chunk$set(echo = TRUE)

Loading the example data

pGRN package pre-loaded with pGRNDB data with both of expression matrix and pseudotime information. You can simply load this data by calling pGRNDB.

# loading pGRN package
library(pGRN)

# loading pre-build data
example_data <- pGRNDB
names(example_data)
expression_matrix <- example_data[["expression"]]
pseudotime_list <- example_data[["ptime"]]$PseudoTime

Call pGRN

Currently, two methods "DTW" and "granger" were available for pGRN network construction.

# try DTW method
nets_dtw <- pGRN(expression_matrix,pseudotime_list, method= "DTW",quantile_cutoff=50)

# try granger method
nets_gg <- pGRN(expression_matrix,pseudotime_list, method= "granger")

plot the network

pGRN provides methods for visualize the network either stationary or interactively.

# plot network stationarily
plot_network(nets_dtw[[1]])
plot_network(nets_gg[[1]])

# plot network interactively
#plot_network_i(nets_dtw[[1]])
#plot_network_i(nets_gg[[1]])

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