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Enrich for drug targets

Source: R/enrich_drug_list.R
enrich_drug_list.Rd

Enrichment analysis for drug targets of multiple gene sets using enrichR, allowing for using different or same background genes for each gene set

Usage

enrich_drug_list(
  gene_list,
  drug_dbs = c("DSigDB", "DrugMatrix"),
  universe = NULL,
  universe_list = NULL,
  pvalueCutoff = 0.05
)

Arguments

gene_list

A list of gene vectors, need to be gene symbols

drug_dbs

A character vector of drug-related databases in enrichR to use for enrichment analysis. Available databases can be checked with enrichR::listEnrichrDbs(). (default is c("DSigDB", "DrugMatrix"))

universe

Background genes for all input gene sets, used if universe_list is not provided

universe_list

Background genes for each input gene set, a list of gene vectors with the same names as gene_list, need to be gene symbols.

pvalueCutoff

(Optional) Adjusted p-value cutoff for filtering enriched terms (default is 0.05)

Value

A data frame of enriched drug targets for each gene set in the input list.

Examples

library(dplyr)
data(example_net)
example_module <- data.frame(Module = as.factor(example_net$colors)) %>%
    tibble::rownames_to_column("Feature") %>% arrange(Module)
example_module_list <- example_module %>% filter(Module != 0) %>%
    split(as.character(.$Module)) %>%
    lapply(`[[`, "Feature")
# drugs_tb = enrich_drug_list(example_module_list, drug_dbs = c("DSigDB"),
#     universe = example_module$Feature, pvalueCutoff = 0.1)