Get all published associations from the GWAS catalog

[privefl]

There are some weird columns.
For now, what I have been able to do:

# 88 MB to download
all_assoc <- bigreadr::fread2(
  "https://www.ebi.ac.uk/gwas/api/search/downloads/full", sep = "\t", na.strings = "")

(table(chr <- sub("^([0-9XYM]+).*$", "\\1", all_assoc$CHR_ID), exclude = NULL))

(pos <- as.numeric(sub("^([0-9XYM]+).*$", "\\1", all_assoc$CHR_POS)))

# Verif
library(dplyr)
data.frame(chr, pos) %>%
  group_by(chr) %>%
  summarise(min(pos), max(pos)) %>%
  arrange(desc(`max(pos)`)) %>%
  print(n = Inf)