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Repair statistics column in a GWAS summary statistics tibble

repair_stats.Rd

repair_stats() is a collection of functions that can be used to infer missing columns in GWAS summary statistics. The functions are based on functionality found online.

Usage

repair_stats(
  tbl,
  dbsnp_path,
  impute_freq = c("None", "EUR", "AMR", "AFR", "SAS", "EAS"),
  impute_freq_file = NULL,
  impute_n = FALSE
)

Arguments

tbl

a data.frame or character() vector

dbsnp_path

filepath to the dbSNP155 directory

impute_freq

one of c("None", "EUR", "AMR", "AFR", "SAS", "EAS"). If None, no imputation is done. Otherwise precomputed alleles frequence from 1000KG, selected ancestry is used

impute_freq_file

filepath to a .parquet file with custom allele frequencies. The file needs to be a tabular dataframe with columns RSID, EffectAllele, OtherAllele, EAF. EAF should correspond to the frequency of the EffectAllele.

impute_n

Should N be imputed if it's missing?

Value

a tibble

Examples

if (FALSE) { # \dontrun{
updated <- repair_stats(my_gwas)
} # }