get_sample_size: Get sample size

In RajLabMSSM/echodata: echoverse module: Fine-mapping data access and formatting

Get sample size

Description

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)

RajLabMSSM/echodata documentation built on Nov. 21, 2023, 8 a.m.