pruning_pleioh2g_wrapper: Perform pruning in computing pleioh2g and correct bias

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

Perform pruning in computing pleioh2g and correct bias

Description

Perform pruning in computing pleioh2g and correct bias

Usage

pruning_pleioh2g_wrapper(
  G,
  phenotype,
  munged_sumstats,
  ld_path,
  wld_path,
  sample_prev = NULL,
  population_prev = NULL,
  n_block = 200,
  hmp3,
  sample_rep
)

Arguments

G	index of target disease.
phenotype	Vector of the phenotype name
munged_sumstats	All LDSC-munged GWAS .stat.gz
ld_path	Path to directory containing ld score files.
wld_path	Path to directory containing weight files.
sample_prev	Vector of sample prevalence, in the same order of input GWAS summary statistics.
population_prev	Vector of population prevalence, in the same order of input GWAS summary statistics.
n_block	number of jackknife blocks.
hmp3	Directory for hapmap 3 snplist.
sample_rep	sampling times in bias correction

Value

A 'list' containing the following elements: - 'target_disease' (character): The value "401.1". - 'target_disease_h2_est' (numeric): target disease h2g. - 'target_disease_h2_se' (numeric): target disease h2g_se. - 'selected_auxD' (character): auxiliary diseases. - 'h2pleio_uncorr' (numeric): pre-correction pleiotropic heritability estimate. - 'h2pleio_uncorr_se' (numeric): pre-correction pleiotropic heritability jackknife s.e. estimate. - 'percentage_h2pleio_uncorr' (numeric): pre-correction percentage of pleiotropic heritability estimate. - 'percentage_h2pleio_uncorr_se' (numeric): pre-correction percentage of pleiotropic heritability jackknife s.e. estimate. - 'percentage_h2pleio_uncorr_jackknife' (numeric): vector of all pre-correction percentage of pleiotropic heritability jackknife estimates. - 'h2pleio_corr' (numeric): post-correction pleiotropic heritability estimate. - 'h2pleio_corr_se' (numeric): post-correction pleiotropic heritability estimate s.e.. - 'percentage_h2pleio_corr' (numeric): post-correction percentage of pleiotropic heritability estimate. - 'percentage_h2pleio_corr_se' (numeric): post-correction percentage of pleiotropic heritability jackknife s.e. estimate. - 'percentage_h2pleio_corr_Z' (numeric): post-correction percentage of pleiotropic heritability estimate Z score. - 'corrected_weight' (numeric): corrected weight in bias correction.

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