compute_sample_size_neff: Compute Neff/N

In neurogenomics/MungeSumstats: Standardise summary statistics from GWAS

Compute Neff/N

Description

Compute Neff/N

Usage

compute_sample_size_neff(
  sumstats_dt,
  method,
  force_new = FALSE,
  append_method_name = FALSE
)

Arguments

sumstats_dt	Summary statistics data.table.
method	Method for computing (effective) sample size. "ldsc" : 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)])) bulik/ldsc GitHub Issue bulik/ldsc GitHub code "giant" : Neff = 2 / (1/N_CAS + 1/N_CON) Winkler et al. 2014, Nature "metal" : Neff = 4 / (1/N_CAS + 1/N_CON) Willer et al. 2010, Bioinformatics "sum" : N = N_CAS + N_CON Simple summation of cases and controls that does not account for class imbalance. "\<integer\>" : N = \<integer\> If method is a positive integer, it will be used as N for every row.
force_new	If "Neff" (or "N") already exists in sumstats_dt, replace it with the recomputed version.
append_method_name	should Neff column have an indicator to explain the method that makes it., Default is FALSE unless multiple methods are passed

Value

No return

neurogenomics/MungeSumstats documentation built on Aug. 10, 2024, 5:59 a.m.