echolocatoR output example: all loci — get_Nalls2019

An example results file after running finemap_loci on all Parkinson's disease (PD)-associated loci.

(NOTE : Formerly merged_DT)

get_Nalls2019_merged()

Format

data.table

SNP: SNP RSID
CHR: Chromosome
POS: Genomic position (in basepairs)
...: Optional: extra columns

Source

https://doi.org/10.1016/S1474-4422(19)30320-5

Details

Data originally comes from the PD GWAS by Nalls et al. (The Lancet Neurology).

Examples

if (FALSE) {
library(dplyr)
local_files <- echodata::portal_query(phenotypes = "parkinson", 
                            file_types = "multi_finemap",
                            LD_panels = "UKB", 
                            nThread = 10, overwrite=TRUE) 
Nalls2019_merged <- lapply(local_files, function(x){ 
message(x)
        if(file.exists(x) && file.size(x)>0){
            dat <- data.table::fread(x)
            dat <- update_cols(dat)
            dat <- find_consensus_snps(dat=dat)
            dat <- assign_lead_snp(dat)
            return(dat)
        }else {return(NULL)}
}) %>% data.table::rbindlist(fill = TRUE) 

#### piggyback ####                  
tmp <- file.path(tempdir(),"Nalls2019_merged.tsv.gz")
data.table::fwrite(Nalls2019_merged,tmp,sep="\t")
piggyback::pb_upload(file = tmp,
                     repo = "RajLabMSSM/echodata")
}