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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)

## [1] "expression" "ptime"

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")

## Time relapsed for granger test: 1.6192889213562 seconds!

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]])

These binaries (installable software) and packages are in development.
They may not be fully stable and should be used with caution. We make no claims about them.
Health stats visible at Monitor.