Gene therapy targets

Identify the overlap between your prioritised list of gene therapy targets and currently existing gene therapy targets that are currently on the market or are in clinical trials. Uses data from the Therapuetic Target Database.

ttd_check(
  top_targets,
  drug_types = NULL,
  failed_status = c("Terminated", "Withdrawn from market", "Discontinued*", NA),
  keep_status = NULL,
  remove_status = c(NA),
  allow.cartesian = FALSE,
  run_map_genes = TRUE,
  force_new = FALSE,
  show_plot = TRUE,
  save_path = NULL,
  height = NULL,
  width = NULL,
  phenotype_to_genes = HPOExplorer::load_phenotype_to_genes()
)

Arguments

top_targets

Top targets generated by prioritise_targets.

drug_types

Filter results by drug type.

failed_status

Drug approval status categories that indicate the drug failed.

keep_status

Filter results by drug approval status.

remove_status

Remove results by drug approval status.

allow.cartesian

See allow.cartesian in [.data.table.

run_map_genes

Map genes to standardised HGNC symbols using map_genes.

force_new

If TRUE, force a new download.

show_plot

Print the plot to the console.

save_path

Save the plot to a file. Set to NULL to not save the plot.

height

Height of the saved plot.

width

Width of the saved plot.

phenotype_to_genes

Phenotype to gene mapping from load_phenotype_to_genes.

Examples

top_targets <- MSTExplorer::example_targets$top_targets
res <- ttd_check(top_targets=top_targets)
#> Loading required namespace: readxl
#> Retrieving all organisms available in gprofiler.
#> Using stored `gprofiler_orgs`.
#> Mapping species name: hsapiens
#> 1 organism identified from search: hsapiens
#> 13,815 / 27,118 (50.94%) genes mapped.
#> Reading cached RDS file: phenotype_to_genes.txt
#> + Version: v2024-12-12
#> Non-failed gene targets enrichment p-value: 8.49288852005138e-18
#> Failed gene targets depletion p-value: 0.0359663542091514