RunCleaner.RdCleans GWAS summary statistics and adds metadata
RunCleaner(sumstats, ColsToKeep, bigSNP)
| sumstats | a tibble or data frame containing raw summary statistics. Coordinates should be hg39/b37; the pipeline does not support hg38. |
|---|---|
| ColsToKeep | character vector of the following columns: chr, position, allele1, allele2, beta, se, unique id, pvalue |
Cleaned summary statistics + LD block of every SNP, as well as its index in the reference panel of genotypes