Annotate the Affected Genes in the Provided Enriched Terms — annotate_term_genes • pathfindR

Function to annotate the involved affected (input) genes in each term.

annotate_term_genes(
  result_df,
  input_processed,
  genes_by_term = pathfindR.data::kegg_genes
)

Arguments

result_df: data frame of enrichment results. The only must-have column is 'ID'.
input_processed: input data processed via input_processing
genes_by_term: List that contains genes for each gene set. Names of this list are gene set IDs (default = kegg_genes)

Value

The original data frame with two additional columns:

Up_regulated: the up-regulated genes in the input involved in the given term's gene set, comma-separated
Down_regulated: the down-regulated genes in the input involved in the given term's gene set, comma-separated

Examples

example_gene_data <- example_pathfindR_input
colnames(example_gene_data) <- c('GENE', 'CHANGE', 'P_VALUE')

annotated_result <- annotate_term_genes(
  result_df = example_pathfindR_output,
  input_processed = example_gene_data
)
#> ## Annotating involved genes and visualizing enriched terms