GWAS Summary Statistics

suppressMessages(library(tidyverse))
webdata_pre = "/Users/haekyungim/Box/LargeFiles/imlab-data/data-Github/web-data/"
work.dir = glue::glue("{webdata_pre}/2021-04-23-gwas-summary-statistics")
if(!file.exists(work.dir)) system(glue::glue("mkdir {work.dir}"))

read Pan-UK Biobank phenotype manifest

## downloaded 4/23/2021 from https://docs.google.com/spreadsheets/d/1AeeADtT0U1AukliiNyiVzVRdLYPkTbruQSk38DeutU8/edit?usp=sharing
PanUKBB_phenotype_manifest =read_csv(glue::glue("{work.dir}/Pan-UK Biobank-phenotype-manifest.csv"),guess_max = 10000)

## 
## ── Column specification ────────────────────────────────────────────────────────
## cols(
##   .default = col_double(),
##   trait_type = col_character(),
##   phenocode = col_character(),
##   pheno_sex = col_character(),
##   coding = col_character(),
##   modifier = col_character(),
##   description = col_character(),
##   description_more = col_character(),
##   coding_description = col_character(),
##   category = col_character(),
##   pops = col_character(),
##   filename = col_character(),
##   filename_tabix = col_character(),
##   aws_link = col_character(),
##   aws_link_tabix = col_character(),
##   wget = col_character(),
##   wget_tabix = col_character(),
##   md5_hex = col_character(),
##   md5_hex_tabix = col_character()
## )
## ℹ Use `spec()` for the full column specifications.

Summary of phenotypes

Trait types

PanUKBB_phenotype_manifest %>% count(trait_type)

## # A tibble: 6 x 2
##   trait_type        n
## * <chr>         <int>
## 1 biomarkers       30
## 2 categorical    3684
## 3 continuous      820
## 4 icd10           915
## 5 phecode        1327
## 6 prescriptions   445

Mostly both_sexes results

PanUKBB_phenotype_manifest %>% count(pheno_sex)

## # A tibble: 3 x 2
##   pheno_sex      n
## * <chr>      <int>
## 1 both_sexes  7089
## 2 females      107
## 3 males         25

chr: Chromosome of the variant.

pos: Position of the variant in GRCh37 coordinates.

ref: Reference allele on the forward strand.

alt: Alternate allele (not necessarily minor allele). Used as effect allele for GWAS.