ldsc_h2: Estimate heritability - refer to ldscr R package...

In pleioh2g: Estimation of Pleiotropic Heritability from Genome-Wide Association Studies (GWAS) Summary Statistics

Estimate heritability - refer to ldscr R package (https://github.com/mglev1n/ldscr)

Description

'ldsc_h2()' uses ldscore regression to estimate the heritability of a trait from GWAS summary statistics and reference LD information.

Usage

ldsc_h2(
  munged_sumstats,
  sample_prev = NA,
  population_prev = NA,
  ld,
  wld,
  n_blocks = 200,
  chisq_max = NA,
  chr_filter = seq(1, 22, 1)
)

Arguments

munged_sumstats	Either a dataframe, or a path to a file containing munged summary statistics. Must contain at least columns named 'SNP' (rsid), 'A1' (effect allele), 'A2' (non-effect allele), 'N' (total sample size) and 'Z' (Z-score)
sample_prev	(numeric) For binary traits, this should be the prevalence of cases in the current sample, used for conversion from observed heritability to liability-scale heritability. The default is 'NA', which is appropriate for quantitative traits or estimating heritability on the observed scale.
population_prev	(numeric) For binary traits, this should be the population prevalence of the trait, used for conversion from observed heritability to liability-scale heritability. The default is 'NA', which is appropriate for quantitative traits or estimating heritability on the observed scale.
ld	(character) Path to directory containing ld score files, ending in '*.l2.ldscore.gz'.
wld	(character) Path to directory containing weight files.
n_blocks	(numeric) Number of blocks used to produce block jackknife standard errors. Default is '200'
chisq_max	(numeric) Maximum value of Z^2 for SNPs to be included in LD-score regression. Default is to set 'chisq_max' to the maximum of 80 and N*0.001.
chr_filter	(numeric vector) Chromosomes to include in analysis. Separating even/odd chromosomes may be useful for exploratory/confirmatory factor analysis.

Value

A [tibble][tibble::tibble-package] containing heritability information. If 'sample_prev' and 'population_prev' were provided, the heritability estimate will also be returned on the liability scale.

pleioh2g documentation built on March 9, 2026, 5:07 p.m.