add_symptom_results: Add symptom results

In neurogenomics/MultiEWCE: Multi-Scale Target Explorer

Add symptom results

Description

Add symptom results to the results data.table.

Usage

add_symptom_results(
  results = load_example_results(),
  q_threshold = 0.05,
  effect_threshold = NULL,
  celltype_col = "CellType",
  ctd_list = load_example_ctd(file = paste0("ctd_", unique(results$ctd), ".rds"),
    multi_dataset = TRUE),
  phenotype_to_genes = HPOExplorer::load_phenotype_to_genes(),
  annotLevels = map_ctd_levels(results),
  keep_quantiles = seq(30, 40),
  top_n = NULL,
  proportion_driver_genes_symptom_threshold = 0.25,
  drop_subthreshold = FALSE
)

Arguments

results	The cell type-phenotype enrichment results generated by gen_results and merged together with merge_results
q_threshold	The q value threshold to subset the results by.
effect_threshold	The minimum fold change in specific expression to subset the results by.
celltype_col	Cell type column name in results.
ctd_list	A named list of CellTypeDataset objects each created with generate_celltype_data.
phenotype_to_genes	Output of load_phenotype_to_genes mapping phenotypes to gene annotations.
annotLevels	The annotation level to use within each CTD in ctd_list.
keep_quantiles	Quantiles to keep in each CellTypeDataset of the ctd_list.
top_n	Top N genes to keep when grouping by group_vars.
proportion_driver_genes_symptom_threshold	The minimum proportion of overlap between symptom genes (genes annotated to a phenotype via a specific disease) and the driver genes (genes driving a signficant phenotype-cell type association).
drop_subthreshold	Drop rows that don't meet the proportion_driver_genes_symptom_threshold criterion.

Examples

results = load_example_results()[seq(5000)]
results <- add_symptom_results()

neurogenomics/MultiEWCE documentation built on Sept. 28, 2024, 2:27 a.m.