LD score regression

Usage

snp_ldsc(
  ld_score,
  ld_size,
  chi2,
  sample_size,
  blocks = 200,
  intercept = NULL,
  chi2_thr1 = 30,
  chi2_thr2 = Inf,
  ncores = 1,
  step1_index = NULL,
  type = c("h2", "rg"),
  w0 = NULL
)

Arguments

ld_score: Vector of LD scores.
ld_size: Number of variants used to compute `ld_score`.
chi2: Vector of chi-squared statistics.
sample_size: Sample size of GWAS corresponding to chi-squared statistics. Possibly a vector, or just a single value.
blocks: Either a single number specifying the number of blocks, or a vector of integers specifying the block number of each `chi2` value. Default is `200` for `snp_ldsc()`, dividing into 200 blocks of approximately equal size. `NULL` can also be used to skip estimating standard errors, which is the default for `snp_ldsc2()`.
intercept: You can constrain the intercept to some value (e.g. 1). Default is `NULL` in `snp_ldsc()` (the intercept is estimated) and is `1` in `snp_ldsc2()` (the intercept is fixed to 1). This is equivalent to parameter `--intercept-h2`.
chi2_thr1: Threshold on `chi2` in step 1. Default is `30`. This is equivalent to parameter `--two-step`.
chi2_thr2: Threshold on `chi2` in step 2. Default is `Inf` (none).
type, w0, step1_index: parameters used when called from snp_ldsc_rg

Value

Vector of 4 values (or only the first 2 if `blocks = NULL`): - `[["int"]]`: LDSC regression intercept, - `[["int_se"]]`: SE of this intercept, - `[["h2"]]`: LDSC regression estimate of (SNP) heritability (also see [coef_to_liab]), - `[["h2_se"]]`: SE of this heritability estimate.