pathfindR (version 1.3.0)

annotate_pathway_DEGs: Annotate the Affected Genes in the Provided Pathways

Description

Annotate the Affected Genes in the Provided Pathways

Usage

annotate_pathway_DEGs(result_df, input_processed, gene_sets = "KEGG",
  custom_genes = NULL)

Arguments

result_df

data frame of enrichment results. The only must-have column is "ID".

input_processed

input data processed via `input_processing`

gene_sets

the gene sets used for enrichment analysis. Possible gene sets are KEGG, Reactome, BioCarta, GO-All, GO-BP, GO-CC, GO-MF or Custom (Default = "KEGG"). If "Custom", the custom_genes argument must be specified.

custom_genes

a list containing the genes involved in each custom gene set. Each element is a vector of gene symbols located in the given pathway. Names correspond to the ID of the pathway.

Value

The original data frame with two additional columns:

Up_regulated

Up-regulated input genes in the given pathway

Down_regulated

Down-regulated input genes in the given pathway

Examples

# NOT RUN {
example_gene_data <- RA_input
colnames(example_gene_data) <- c("GENE", "CHANGE", "P_VALUE")

annotated_result <- annotate_pathway_DEGs(RA_output, example_gene_data)

# }