pruning_pleioh2g_wrapper: 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
)

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 jackknife s.e. estimate. - `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. - `corrected_weight` (numeric): corrected weight in bias correction.

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