ldsc_rg: Cross-Trait LD score regression

In jean997/sumstatFactors: Genetic Factor Analysis (GFA)

Cross-Trait LD score regression

Description

Cross-Trait LD score regression

Usage

ldsc_rg(
  ld_score,
  ld_size,
  z1,
  z2,
  sample_size_1,
  sample_size_2,
  blocks = 200,
  h2_1 = NULL,
  h2_2 = NULL,
  intercept = NULL,
  intercept_h2_1 = NULL,
  intercept_h2_2 = NULL,
  step1_chisq_max = 30,
  chi2_thr2 = Inf,
  ncores = 1,
  h2_se = FALSE
)

Arguments

ld_score	Vector of LD scores.
ld_size	Number of variants used to compute 'ld_score'.
z1	Vector of z-scores for trait 1.
z2	Vector of z-scores for trait 2.
sample_size_1	Sample size of GWAS for trait 1. Possibly a vector, or just a single value.
sample_size_2	Sample size of GWAS for trait 2. 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. 0). Default is 'NULL' (the intercept is estimated). Use a value of 0 if you are sure there is no overlap between GWAS samples.
intercept_h2_1	Intercept for heritability of trait 1 (default is NULL so the intercept is estimated).
intercept_h2_2	Intercept for heritability of trait 2 (default is NULL so the intercept is estimated).
step1_chisq_max	Threshold on 'chi2' in step 1. Default is '30'.
chi2_thr2	Threshold on 'chi2' in step 2. Default is 'Inf' (none).

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 - '[["h2_se"]]': SE of this heritability estimate.

jean997/sumstatFactors documentation built on April 15, 2024, 6:39 p.m.