snp_ldsc: LD score regression

In jean997/sumstatFactors: Genetic Factor Analysis (GFA)

LD score regression

Description

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.

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