ttd_check: Gene therapy targets

In neurogenomics/MultiEWCE: Multi-Scale Target Explorer

Gene therapy targets

Description

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 Therapeutic Target Database.

Usage

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  failed_status = c("Terminated", "Withdrawn from market", "Discontinued*", NA),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 = FALSE,
  add_descriptions = FALSE,
  force_new = FALSE,
  as_percent = TRUE,
  base_size = 9,
  label_size = 2,
  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.
add_descriptions	Add disease names and descriptions.
force_new	If TRUE, force a new download.
as_percent	Show the plot's y-axis as a percentage within each x-axis group (TRUE). Otherwise, show y-axis as the number of drugs within that x-axis group.
base_size	Base size for ggplot2 theme.
label_size	Size of labels in plot.
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,
                 run_map_genes=FALSE)

neurogenomics/MultiEWCE documentation built on April 17, 2025, 9:27 p.m.