Create Kappa Statistics Matrix
create_kappa_matrix(
enrichment_res,
use_description = FALSE,
use_active_snw_genes = FALSE
)
data frame of pathfindR enrichment results. Must-have
columns are "Term_Description" (if use_description = TRUE
) or "ID"
(if use_description = FALSE
), "Down_regulated", and "Up_regulated".
If use_active_snw_genes = TRUE
, "non_Signif_Snw_Genes" must also be
provided.
Boolean argument to indicate whether term descriptions
(in the "Term_Description" column) should be used. (default = FALSE
)
boolean to indicate whether or not to use non-input active subnetwork genes in the calculation of kappa statistics (default = FALSE, i.e. only use affected genes)
a matrix of kappa statistics between each term in the enrichment results.
sub_df <- RA_output[1:3, ]
create_kappa_matrix(sub_df)
#> hsa05415 hsa04130 hsa03410
#> hsa05415 1.0000000 -0.3636364 -0.3255814
#> hsa04130 -0.3636364 1.0000000 -0.2272727
#> hsa03410 -0.3255814 -0.2272727 1.0000000