Generate ORA results for a network and a given number of permutations
webgestalt_network.RdGiven a network or network subset, webgestalt_network will generate Over-Representation Analysis (ORA)
results for this network and a given number of permutations. These are stored in a directory named "network_name"
within the specified output_directory, which contains a folder "p0" for the input network and folders "p1", "p2",
and so on for the different permutations of the network. Within these folders are .csv files for each source node.
These files contain information on the gene set terms that are the most over-represented in the source node's targets.
This function also creates a "webgestalt_work" directory in the output_directory, which has the same structure as
the "network_name" directory, but the files are .txt files containing the list of targets for each source node.
Usage
webgestalt_network(
network_path,
reference_set,
output_directory,
network_name,
organism = "hsapiens",
database = "geneontology_Biological_Process_noRedundant",
gene_id = "ensembl_gene_id",
permutations = 10
)Arguments
- network_path
path to the network or network subset to evaluate. Must be a tab-separated file where the first column is the source nodes (TFs) and the second column is the target nodes (regulated genes).
- reference_set
path to the set of all genes possibly included in the network. Must be a .txt file containing exactly one column of the genes that could possibly appear in the network.
- output_directory
path to the directory in which output should be stored. It is recommended to make a dedicated directory for the output from all network subsets of a single original network.
- network_name
the name of the directory to store the results within the output_directory. It should be in the same format as the files output by
subset_network: "{name}_{# of edges}" i.e. "example_8".- organism
a string specifying the organism that the data is from, e.g. "hsapiens" or "scerevisiae" - see options with WebGestaltR::listOrganism()
- database
the gene set database to search for enrichment - see options with WebGestaltR::listGeneSet()
- gene_id
the naming system used for the input genes - see options with WebGestaltR::listIdType() and see webgestalt.org for examples of each type
- permutations
the number of randomly permuted networks to create and run ORA on