Perform the whole GOeval pipeline on one network
evaluate.RdGiven one network, evaluate will first make subsets with subset_network,
then run Over-Representation Analysis (ORA) with webgestalt_network,
followed by get_metrics and plot_metrics to plot selected summary
statistics.
Usage
evaluate(
network,
reference_set,
output_directory,
network_name,
organism = "hsapiens",
database = "geneontology_Biological_Process_noRedundant",
gene_id = "ensembl_gene_id",
edges = c(512, 1024, 2048, 4096, 8192, 16384, 32768, 65536),
num_possible_TFs = 0,
permutations = 3,
penalty = 3,
fdr_threshold = 0.05,
get_sum = TRUE,
get_percent = FALSE,
get_mean = FALSE,
get_median = FALSE,
get_annotation_overlap = FALSE,
get_size = TRUE,
plot = TRUE
)Arguments
- network
path to the file containing the network to create subsets from. The file should be tab-separated with three columns: source node, target node, edge score
- 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 to store the generated network subsets, ORA summaries, and plots
- network_name
short name for the network - used in file naming so may not contain spaces
- 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(). Must be a Gene Ontology "biological process" database if get_annotation_overlap = TRUE.
- gene_id
the naming system used for the input genes - see options with WebGestaltR::listIdType() and see webgestalt.org for examples of each type
- edges
list of total numbers of edges or average edges per TF to include in each subset
- num_possible_TFs
if set to a number > 0, the elements of 'edges' will first be multiplied by this number to get the number of edges for each subset
- permutations
the number of randomly permuted networks to create and run ORA on
- penalty
the penalty applied to the 'sum' metric for each TF in the network
- fdr_threshold
the FDR threshold for a gene set term to be considered significantly over-represented for the purposes of calculating the 'percent' metric
- get_sum
boolean whether to get and plot the 'sum' metric, which is the sum of the negative log base 10 of the p-value for the top term of each source node minus 'penalty' times the total number of source nodes.
- get_percent
boolean whether to get and plot the 'percent' metric, which is the percent of source nodes with at least one term with a FDR below the 'fdr_threshold'
- get_mean
boolean whether to get and plot the 'mean' metric, which is the mean negative log base 10 of the p-value for the top term of each source node regardless of significance
- get_median
boolean whether to get and plot the 'median' metric, which is the median negative log base 10 of the p-value for the top term of each source node regardless of significance
- get_annotation_overlap
boolean whether to get and plot the 'annotation_overlap' metric, which is the percent of source nodes that are annotated to at least one of the 16 GO terms for which their target genes are most enriched
- get_size
boolean whether to get and plot the 'size' metric, which is the number of source nodes in the network subset that have more than one target gene with annotations. This number is used in the calculation of all other metrics.
- plot
boolean whether to make plots of the calculated metrics and write them to a pdf