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

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Documentation for package ‘pleioh2g’ version 0.1.0

• DESCRIPTION file.
• User guides, package vignettes and other documentation.

Help Pages

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.
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
Cal_cor_pleiotropic_h2_single	Compute single pleioh2g for target disease before correction with referred disease index in the rg matrix
Cal_cor_test_single	Compute inversed elements for the target disease in bias correction procedure 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
generate_proposal_sample_changea_cor	Generate samples based on sampling covariance matrix and rg matrix for target disease
h2_liability	Convert Heritability to Liability Scale
h2_vector_15D	h2 vector for 15 diseases
h2_vector_mat_15D	h2 jk matrix for 15 diseases
ldsc_h2	Estimate heritability - refer to ldscr R package (https://github.com/mglev1n/ldscr)
ldsc_rg	Estimate cross-trait genetic correlations (Robust Version) - refer to ldscr R package (https://github.com/mglev1n/ldscr)
make_weights	Internal Function to make weights - refer to ldscr R package (https://github.com/mglev1n/ldscr)
merge_sumstats	Merging summary statistics with LD-score files - refer to ldscr R package (https://github.com/mglev1n/ldscr)
perform_analysis	Internal function to perform LDSC heritability/covariance analysis - refer to ldscr R package (https://github.com/mglev1n/ldscr)
pleiotropyh2_cor_computing_single	Compute pleioh2g after bias correction for target disease
pleiotropyh2_cor_computing_single_prune	Compute pleioh2g after bias correction for target disease
pleiotropyh2_nocor_computing_single	Compute pleioh2g before bias correction for target disease
Prune_disease_selection_DTrgzscore	Prune disease selection
pruning_pleioh2g_wrapper	Perform pruning in computing pleioh2g and correct bias
read_ld	Read ld from either internal or external file - refer to ldscr R package (https://github.com/mglev1n/ldscr)
read_m	Read M from either internal or external file - refer to ldscr R package (https://github.com/mglev1n/ldscr)
read_sumstats	Read summary statistics from either internal or external file - refer to ldscr R package (https://github.com/mglev1n/ldscr)
read_wld	Read wld from either internal or external file - 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)
Rg_mat_z_15D	Genetic correlation Z matrix for 15 diseases
sumstats_munged_example_input	Example munged dataframe - refer to ldscr R package (https://github.com/mglev1n/ldscr)