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

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

## Documentation for package ‘pleioh2g’ version 0.1.3

- 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 | h2 vector for 62 traits
h2_vector_mat | h2 jk matrix for 62 traits
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 | Genetic correlation matrix for 62 traits
Results_full_rg_array | Jackknife array of genetic correlations (62 traits)
Rg_mat_z | Genetic correlation Z matrix for 62 traits
sumstats_munged_example_input | Example munged dataframe - refer to ldscr R package (https://github.com/mglev1n/ldscr)