## ----include = FALSE----------------------------------------------------------
knitr::opts_chunk$set(
  collapse = TRUE,
  comment = "#>",
  eval = FALSE
)

## ----setup--------------------------------------------------------------------
# library(unitcm)
# library(dplyr)

## ----sources------------------------------------------------------------------
# sources <- fetch_midas_sources()
# sources
# 
# stats <- fetch_midas_stats()
# cat(stats$total_associations, "associations across",
#     stats$total_genes, "genes and",
#     stats$total_diseases, "diseases\n")

## ----gene-to-disease----------------------------------------------------------
# genes <- c("TP53", "BRCA1", "EGFR", "VEGFA", "MYC")
# 
# results <- query_gene_diseases(
#   genes,
#   min_sources = 2,
#   scoring_method = "max"
# )
# 
# head(results, 10)
# 
# # Gene ID resolution mapping
# attr(results, "gene_mapping")

## ----disease-to-gene----------------------------------------------------------
# results <- query_disease_genes(
#   "breast cancer",
#   min_sources = 3,
#   page_size = 50
# )
# 
# head(results, 10)
# 
# # Which diseases were matched?
# attr(results, "matched_diseases")

## ----enrichment---------------------------------------------------------------
# gene_list <- c("TP53", "BRCA1", "EGFR", "VEGFA", "MYC", "KRAS",
#                "AKT1", "PIK3CA", "PTEN", "RB1")
# 
# enrichment <- query_disease_enrichment(
#   gene_list,
#   p_value_cutoff = 0.05,
#   correction_method = "fdr",
#   min_hit_count = 3
# )
# 
# cat(attr(enrichment, "total_significant"), "significant diseases from",
#     attr(enrichment, "total_tested"), "tested\n")
# 
# head(enrichment, 10)

## ----convert------------------------------------------------------------------
# mixed_ids <- c("TP53", "7157", "ENSG00000141510", "BRCA1")
# converted <- convert_gene_ids(mixed_ids)
# converted

## ----source-comparison--------------------------------------------------------
# comparison <- query_source_comparison(
#   c("TP53", "BRCA1", "EGFR"),
#   mode = "union"
# )
# 
# # Genes covered by each source
# lapply(comparison$sets, length)
# 
# # Exclusive to each source
# comparison$exclusives

## ----disease-intersection-----------------------------------------------------
# intersection <- query_disease_intersection(
#   c("breast cancer", "lung cancer", "colorectal cancer")
# )
# 
# cat(intersection$total_intersection_genes, "genes shared across all diseases\n")
# head(intersection$targets)

## ----autocomplete-------------------------------------------------------------
# autocomplete_disease("diabet")
# autocomplete_disease("breast")