Get sample size

Infer sample size from summary stats using MungeSumstats.

Usage

get_sample_size(
  dat,
  compute_n = c("ldsc", "giant", "metal", "sum"),
  return_only = NULL,
  force_new = FALSE,
  standardise_headers = FALSE,
  verbose = TRUE,
  ...
)

Arguments

dat

Fine-mapping results data.

compute_n

How to compute per-SNP sample size (new column "N").
If the column "N" is already present in dat, this column will be used to extract per-SNP sample sizes and the argument compute_n will be ignored.
If the column "N" is not present in dat, one of the following options can be supplied to compute_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).

return_only

A function to return only a single value from the inferred/imputed sample size column (e.g. max, min).

force_new

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

standardise_headers

Standardise headers first.

verbose

Print messages.

...

Additional argument passed to return_only function, if return_only is not NULL.

Examples

dat <- echodata::BST1
dat2 <- echodata::get_sample_size(dat = dat)
#> Preparing sample size column (N).
#> Computing effective sample size using the LDSC method:
#>  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)]))
#> + Mapping colnames from MungeSumstats ==> echolocatoR