Check for N column if not present and user wants, impute N based on user's sample size. NOTE this will be the same value for each SNP which is not necessarily correct and may cause issues down the line. N can also be inputted with "ldsc", "sum", "giant" or "metal" by passing one or multiple of these.

Source: R/compute_nsize.R

Check for N column if not present and user wants, impute N based on user's sample size. NOTE this will be the same value for each SNP which is not necessarily correct and may cause issues down the line. N can also be inputted with "ldsc", "sum", "giant" or "metal" by passing one or multiple of these.

compute_nsize(
  sumstats_dt,
  imputation_ind = FALSE,
  compute_n = c("ldsc", "giant", "metal", "sum"),
  standardise_headers = FALSE,
  force_new = FALSE,
  return_list = TRUE
)

Arguments

sumstats_dt

data table obj of the summary statistics file for the GWAS.

imputation_ind

Binary Should a column be added for each imputation step to show what SNPs have imputed values for differing fields. This includes a field denoting SNP allele flipping (flipped). Note these columns will be in the formatted summary statistics returned. Default is FALSE.

compute_n

How to compute per-SNP sample size (new column "N").

  • 0: N will not be computed.

  • >0: If any number >0 is provided, that value will be set as N for every row. Note: Computing N this way is incorrect and should be avoided if at all possible.

  • "sum": N will be computed as: cases (N_CAS) + controls (N_CON), so long as both columns are present.

  • "ldsc": N will be computed as effective sample size: Neff =(N_CAS+N_CON)*(N_CAS/(N_CAS+N_CON)) / mean((N_CAS/(N_CAS+N_CON))(N_CAS+N_CON)==max(N_CAS+N_CON)).

  • "giant": N will be computed as effective sample size: Neff = 2 / (1/N_CAS + 1/N_CON).

  • "metal": N will be computed as effective sample size: Neff = 4 / (1/N_CAS + 1/N_CON).

standardise_headers

Standardise headers first.

force_new

If "Neff" (or "N") already exists in sumstats_dt, replace it with the recomputed version.

return_list

Return the sumstats_dt within a named list (default: TRUE).

Value

list("sumstats_dt"=sumstats_dt)

Examples

sumstats_dt <- MungeSumstats::formatted_example()
#> Standardising column headers.
#> First line of summary statistics file: 
#> MarkerName	CHR	POS	A1	A2	EAF	Beta	SE	Pval	
#> Sorting coordinates.
sumstats_dt2 <- MungeSumstats::compute_nsize(sumstats_dt=sumstats_dt,
                                             compute_n=10000)
#> Assigning N=10000 for all SNPs.