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pleioh2g (version 0.1.0)

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

Description

Provides tools to compute unbiased pleiotropic heritability estimates of complex diseases from genome-wide association studies (GWAS) summary statistics. We estimate pleiotropic heritability from GWAS summary statistics by estimating the proportion of variance explained from an estimated genetic correlation matrix (Bulik-Sullivan et al. 2015 ) and employing a Monte-Carlo bias correction procedure to account for sampling noise in genetic correlation estimates.

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Version

Install

install.packages('pleioh2g')

Monthly Downloads

239

Version

0.1.0

License

GPL-3

Maintainer

Yujie Zhao

Last Published

October 28th, 2025

Functions in pleioh2g (0.1.0)

pleiotropyh2_nocor_computing_single

Compute pleioh2g before bias correction for target disease

pleiotropyh2_cor_computing_single_prune

Compute pleioh2g after bias correction for target disease

pruning_pleioh2g_wrapper

Perform pruning in computing pleioh2g and correct bias

Convert Heritability to Liability Scale

generate_proposal_sample_changea_cor

Generate samples based on sampling covariance matrix and rg matrix for target disease

h2 vector for 15 diseases

h2_vector_mat_15D

h2 jk matrix for 15 diseases

sumstats_munged_example_input

Example munged dataframe - refer to ldscr R package (https://github.com/mglev1n/ldscr)

Read wld from either internal or external file - refer to ldscr R package (https://github.com/mglev1n/ldscr)

Read ld from either internal or external file - refer to ldscr R package (https://github.com/mglev1n/ldscr)

Estimate cross-trait genetic correlations (Robust Version) - refer to ldscr R package (https://github.com/mglev1n/ldscr)

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

Read M from either internal or external file - refer to ldscr R package (https://github.com/mglev1n/ldscr)

Read summary statistics from either internal or external file - refer to ldscr R package (https://github.com/mglev1n/ldscr)

Cal_cor_pleiotropic_h2_corrected_single

Compute single pleioh2g for target disease after correction with referred disease index in the rg matrix and corrected ratio

Genetic correlation Z matrix for 15 diseases

Prune_disease_selection_DTrgzscore

Prune disease selection

Cal_cor_pleiotropic_h2_single

Compute single pleioh2g for target disease before correction with referred disease index in the rg matrix

Cal_rg_h2g_alltraits

Compute rg + h2g

Cal_rg_h2g_jk_alltraits

genomic-block jackknife and compute rg + h2g

Cal_cor_test_single

Compute inversed elements for the target disease in bias correction procedure with referred disease index in the rg matrix

Cal_cor_pleiotropic_h2

Compute a vector of pleioh2g for all diseases before correction This function computes pleioh2g for all diseases before correction in one go.

pleiotropyh2_cor_computing_single

Compute pleioh2g after bias correction for target disease

Internal Function to make weights - refer to ldscr R package (https://github.com/mglev1n/ldscr)

Merging summary statistics with LD-score files - refer to ldscr R package (https://github.com/mglev1n/ldscr)

Results_full_rg_15D

Genetic correlation matrix for 15 diseases

Results_full_rg_array_15D

Jackknife array of genetic correlations (15 diseases)

perform_analysis

Internal function to perform LDSC heritability/covariance analysis - refer to ldscr R package (https://github.com/mglev1n/ldscr)