pathfindR (version 1.3.0)

create_kappa_matrix: Create Kappa Statistics Matrix

Description

Create Kappa Statistics Matrix

Usage

create_kappa_matrix(enrichment_res, use_names = FALSE,
  use_active_snw_genes = FALSE)

Arguments

enrichment_res

data frame of pathway enrichment results. Must-have columns are "Pathway" or "ID", "Down_regulated", and "Up_regulated". If `use_active_snw_genes = TRUE`, "non_DEG_Active_Snw_Genes" must also be provided.

use_names

boolean to indicate whether to use pathway names instead of IDs (default = FALSE, i.e. use IDs)

use_active_snw_genes

boolean to indicate whether or not to use non-input active subnetwork genes in the calculation of kappa statistics (default = FALSE, i.e. use only affected genes)

Value

a matrix of kappa statistics between each term in the enrichment results.

Examples

# NOT RUN {
sub_df <- RA_output[1:3,]
create_kappa_matrix(sub_df)
# }