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"
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: 1.72707581520081 seconds!