## 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]])