GWAS catalog analysis 2022

suppressMessages(library(tidyverse))
suppressMessages(library(glue))
PRE = "/Users/haekyungim/Library/CloudStorage/Box-Box/LargeFiles/imlab-data/data-Github/web-data"
## COPY THE DATA AND SLUG FROM THE HEADER
DATA = glue("{PRE}/2022-04-20-gwas-catalog-analysis-2022")
if(!file.exists(DATA)) system(glue("mkdir {DATA}"))
WORK=DATA

## download data from GWAS catalog
## https://www.ebi.ac.uk/gwas/docs/file-downloads
## move data to DATA
DATAFILE = "gwas_catalog_v1.0.2-associations_e105_r2022-04-07.tsv"
#tempodata=("~/Downloads/tempo/gwas_catalog_v1.0.2-associations_e105_r2022-04-07.tsv")
#system(glue("cp {tempodata} {DATA}/"))

gwascatalog = read_tsv(glue("{DATA}/{DATAFILE}"))

## Warning: One or more parsing issues, see `problems()` for details

## Rows: 372752 Columns: 38

## ── Column specification ────────────────────────────────────────────────────────
## Delimiter: "\t"
## chr  (26): FIRST AUTHOR, JOURNAL, LINK, STUDY, DISEASE/TRAIT, INITIAL SAMPLE...
## dbl  (10): PUBMEDID, CHR_POS, UPSTREAM_GENE_DISTANCE, DOWNSTREAM_GENE_DISTAN...
## date  (2): DATE ADDED TO CATALOG, DATE

## 
## ℹ Use `spec()` to retrieve the full column specification for this data.
## ℹ Specify the column types or set `show_col_types = FALSE` to quiet this message.

dim(gwascatalog)

## [1] 372752     38

names(gwascatalog)

##  [1] "DATE ADDED TO CATALOG"      "PUBMEDID"                  
##  [3] "FIRST AUTHOR"               "DATE"                      
##  [5] "JOURNAL"                    "LINK"                      
##  [7] "STUDY"                      "DISEASE/TRAIT"             
##  [9] "INITIAL SAMPLE SIZE"        "REPLICATION SAMPLE SIZE"   
## [11] "REGION"                     "CHR_ID"                    
## [13] "CHR_POS"                    "REPORTED GENE(S)"          
## [15] "MAPPED_GENE"                "UPSTREAM_GENE_ID"          
## [17] "DOWNSTREAM_GENE_ID"         "SNP_GENE_IDS"              
## [19] "UPSTREAM_GENE_DISTANCE"     "DOWNSTREAM_GENE_DISTANCE"  
## [21] "STRONGEST SNP-RISK ALLELE"  "SNPS"                      
## [23] "MERGED"                     "SNP_ID_CURRENT"            
## [25] "CONTEXT"                    "INTERGENIC"                
## [27] "RISK ALLELE FREQUENCY"      "P-VALUE"                   
## [29] "PVALUE_MLOG"                "P-VALUE (TEXT)"            
## [31] "OR or BETA"                 "95% CI (TEXT)"             
## [33] "PLATFORM [SNPS PASSING QC]" "CNV"                       
## [35] "MAPPED_TRAIT"               "MAPPED_TRAIT_URI"          
## [37] "STUDY ACCESSION"            "GENOTYPING TECHNOLOGY"

## show number of entries in the GWAS catalog with cancer
gwascatalog %>% select(`DISEASE/TRAIT`, MAPPED_GENE) %>% filter(grepl("cancer",`DISEASE/TRAIT`)) %>% dim()

## [1] 7729    2

Number of distinct loci reported in GWAS of various cancers

Number of entries in the GWAS catalog with cancer, unique loci (it’s a reasonable assumption that mapped genes will be a good way to count loci)

gwascatalog %>% select(`DISEASE/TRAIT`, MAPPED_GENE) %>% filter(grepl("cancer",`DISEASE/TRAIT`)) %>% unique() %>% dim()

## [1] 4911    2