Description Usage Arguments Value Examples
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 runPanda
in this package and finds the sets of nodes that best characterize the change in modular structure.
1 | runAlpaca(panda_net1, panda_net2, file.stem, verbose = F)
|
panda_net1 |
Data Frame indicating one entire network generate by |
panda_net2 |
Data Frame indicating another entire network generate by |
file.stem |
The folder location and title under which all results will be stored. |
verbose |
Indicates whether the full differential modularity matrix should also be written to a file. Defaults to FALSE. |
A string message showing the location of output file if file.stem is given, or a List where first element is the membership vector and second element is the contribution score of each node to its module's total differential modularity
1 2 3 4 5 6 7 8 9 10 11 12 13 | # refer to four input datasets files in inst/extdat
treated_expression_file_path <- system.file("extdata", "expr4.txt", package = "netZoo", mustWork = TRUE)
control_expression_file_path <- system.file("extdata", "expr10.txt", package = "netZoo", mustWork = TRUE)
motif_file_path <- system.file("extdata", "chip.txt", package = "netZoo", mustWork = TRUE)
ppi_file_path <- system.file("extdata", "ppi.txt", package = "netZoo", mustWork = TRUE)
# Run PANDA for treated and control network
treated_panda_net <- runPanda(e = treated_expression_file_path, m = motif_file_path, ppi = ppi_file_path, rm_missing = TRUE )$panda
control_panda_net <- runPanda(e = control_expression_file_path, m = motif_file_path, ppi = ppi_file_path, rm_missing = TRUE )$panda
# Run ALPACA
alpaca<- runAlpaca(treated_panda_net, control_panda_net, "~/Desktop/TB", verbose=T)
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