check_on_ref_genome {MungeSumstats} | R Documentation |
Ensure all SNPs are on the reference genome
check_on_ref_genome(sumstats_dt, path, ref_genome, on_ref_genome, rsids)
sumstats_dt |
data table obj of the summary statistics file for the GWAS |
path |
Filepath for the summary statistics file to be formatted |
ref_genome |
name of the reference genome used for the GWAS (GRCh37 or GRCh38). Default is GRCh37. |
on_ref_genome |
Binary Should a check take place that all SNPs are on the reference genome by SNP ID. Default is TRUE |
rsids |
datatable of snpsById, filtered to SNPs of interest if loaded already. Or else NULL |
A list containing two data tables:
sumstats_dt
: the modified summary statistics data table object
rsids
: snpsById, filtered to SNPs of interest if loaded already. Or else NULL