echolocatoR output example (LRRK2 locus)

Source: R/data.R

An example results file after running finemap_loci on the LRRK2 locus.

LRRK2

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: BST1, MEX3C

Examples

if (FALSE) {
root_dir <- "~/Desktop/Fine_Mapping/Data/GWAS/Nalls23andMe_2019"
locus_dir <- "LRRK2/Multi-finemap/Multi-finemap_results.txt"
LRRK2 <- data.table::fread(file.path(root_dir,locus_dir))
LRRK2 <- update_CS_cols(finemap_dat=LRRK2) 
LRRK2 <- find_consensus_SNPs(finemap_dat=LRRK2)
data.table::fwrite(LRRK2,"inst/extdata/Nalls23andMe_2019/LRRK2_Nalls23andMe_2019_subset.tsv.gz", sep="\t")
usethis::use_data(LRRK2, overwrite = T)
}