ALPACA(ALtered Partitions Across Community Architectures) is a method for comparing two genome-scale networks derived from different phenotypic states to identify condition-specific modules.
[(Padi and Quackenbush 2018)])
This function compares two networks generate by pandaPy in this package and finds the sets of nodes that best characterize the change in modular structure.
Arguments
- panda.net1
data.frame indicating an complete network of one condition generated by
pandaPy- panda.net2
data.frame indicating an complete network of another condition generated by
pandaPy- file.stem
String indicating the folder path and prefix of result files, where all results will be stored.
- verbose
Boolean vector indicating whether the full differential modularity matrix should also be written to a file. The default values is 'FALSE'.
Value
A string message showing the location of output file if file.stem is given, and a List where the first element is the membership vector and second element is the contribution score of each node to its module's total differential modularity
Examples
# refer to four input datasets files in inst/extdat
treated_expression_file_path <- system.file("extdata", "expr4_matched.txt",
package = "netZooR", mustWork = TRUE)
control_expression_file_path <- system.file("extdata", "expr10_matched.txt",
package = "netZooR", mustWork = TRUE)
motif_file_path <- system.file("extdata", "chip_matched.txt", package = "netZooR", mustWork = TRUE)
ppi_file_path <- system.file("extdata", "ppi_matched.txt", package = "netZooR", mustWork = TRUE)
# Run PANDA for treated and control network
# \donttest{
treated_panda_net <- pandaPy(expr_file = treated_expression_file_path,
motif_file = motif_file_path, ppi_file = ppi_file_path,
modeProcess="legacy", remove_missing = TRUE )$panda
control_panda_net <- pandaPy(expr_file = control_expression_file_path,
motif_file = motif_file_path, ppi_file = ppi_file_path,
modeProcess="legacy", remove_missing = TRUE )$panda
# Run ALPACA
alpaca<- pandaToAlpaca(treated_panda_net, control_panda_net, "./TB", verbose=TRUE)
# }