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Calculate heritability using LDAK

Source: R/ldak_h2.R
ldak_h2.Rd

This function wraps LDAK, a command-line tool for estimating heritability. The tool and associated reference files can be download from the LDAK website (https://ldak.org/). The method is described in Zhang et al. (Nature Communications 2021; <https://doi.org/10.1038/s41467-021-24485-y).

Usage

ldak_h2(
  sumstats_file,
  ldak_bin,
  ldak_tagfile,
  sample_prev = NULL,
  population_prev = NULL,
  hm3_file,
  ldak_cutoff = 0.01
)

Arguments

sumstats_file

Path to "munged" GWAS summary statistics file in LDSC format. The current implementation of this function requires rsids to link to other LDAK files.

ldak_bin

Path to LDAK binary

ldak_tagfile

Path to LDAK tagfile

sample_prev

Sample prevalence of cases (for case-control studies), NULL (default) for quantitative traits

population_prev

Population prevalence of cases in the sample (for case-control studies), NULL (default) for quantitative traits

hm3_file

Path to hm3 file containing

ldak_cutoff

Minor allele frequency cutoff (default = 0.01)

Value

List of dataframes containing LDAK results

Examples

if (FALSE) {
ldak_h2(sumstats_file = "/path/to/munged_sumstats", ldak_bin = "/path/to/ldak", ldak_tagfile = "/path/to/tagfile",  hm3_file = "/path/to/hm3")
}