check_allele_flip {MungeSumstats} | R Documentation |
Ensure A1 & A2 are correctly named, if GWAS constructed as Risk/nonrisk alleles this will need to be converted
check_allele_flip(sumstats_dt, path, ref_genome, rsids, allele_flip_check)
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) |
rsids |
datatable of snpsById, filtered to SNPs of interest if loaded already. Or else NULL |
allele_flip_check |
Binary Should the allele columns be chacked against reference genome to infer if flipping is necessary. Default is TRUE |
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