echolocatoR output example (BST1 locus)

Source: R/data.R

An example results file after running finemap_loci on the BST1 locus.

BST1

Format

data.table

SNP

SNP RSID

CHR

Chromosome

POS

Genomic positiion (in basepairs)

...

Source

https://www.biorxiv.org/content/10.1101/388165v3

Details

Data originally comes from the Parkinson's disease GWAS by Nalls et al. (bioRxiv).

See also

Other Nalls23andMe_2019: LRRK2, MEX3C

Examples

if (FALSE) {
root_dir <- "~/Desktop/Fine_Mapping/Data/GWAS/Nalls23andMe_2019"
locus_dir <- "BST1/Multi-finemap/Multi-finemap_results.txt"
BST1 <- data.table::fread(file.path(root_dir,locus_dir))
BST1 <- update_CS_cols(finemap_dat=BST1) 
BST1 <- find_consensus_SNPs(finemap_dat=BST1)
data.table::fwrite(BST1,"inst/extdata/Nalls23andMe_2019/BST1_Nalls23andMe_2019_subset.tsv.gz", sep="\t")
usethis::use_data(BST1, overwrite = T)
}