Anthro_LDSC: Anthropometric Genomic SEM LDSC dataset.

In umx: Structural Equation Modeling and Twin Modeling in R

Anthropometric Genomic SEM LDSC dataset.

Description

A dataset containing the genetic covariance structure from LD score regression (LDSC) for 9 anthropometric phenotypes: BMI, WHR, CO, Waist, Hip, Height, IHC, BL, and BW. Same list layout as Psych_LDSC - pass the object as covstruc to umxGSEM() or umxGSEM_GWAS().

Usage

data(Anthro_LDSC)

Format

A list with elements S, V, I, N, and m (see Details).

Details

LDSC list fields (same S/V/I/N/m layout as GenomicSEM ldsc; V names are OpenMx residual labels):

• S: 9 x 9 genetic covariance matrix among the phenotypes (diagonals are SNP heritabilities on the LDSC scale).

• V: 45 x 45 sampling covariance of the unique elements of S (OpenMx vech order; dimnames like var_BMI, poly_WHR_BMI). Used as asymptotic covariance for WLS/DWLS. Not GenomicSEM BMI_BMI / WHR_BMI.

• I: 9 x 9 LDSC intercept matrix. Diagonal = per-trait LDSC intercepts (expected near 1 without confounding; elevations can flag stratification). Off-diagonal = cross-trait intercepts reflecting sample overlap. Used for genomic control when expanding SNPs in umxGSEM_GWAS().

• N: 1 x 45 effective sample sizes for each unique S element.

• m: Number of SNPs used in LDSC (here 1,173,569).

See Also

Psych_LDSC, umxGSEM(), umxGSEM_GWAS(), umxGSEM_ldsc()

Other GSEM: Psych_LDSC, plot.umx_GWAS(), umxGSEM(), umxGSEM_GWAS(), umxGSEM_dl_tutorial_files(), umxGSEM_label_ldsc(), umxGSEM_ldsc(), umxGSEM_munge(), umxGSEM_std(), umxGSEM_sumstats(), umxSummary.MxDataStatic(), umxSummary.list()

Other datasets: Fischbein_wt, GFF, HSwls, Psych_LDSC, docData, iqdat, umx, us_skinfold_data

Examples

## Not run: 
data(Anthro_LDSC)
str(Anthro_LDSC, max.level = 1)
names(Anthro_LDSC) # S, V, I, N, m
# I = LDSC intercepts (diag) and cross-trait intercepts (off-diag)
Anthro_LDSC$I[1:3, 1:3]

## End(Not run)

umx documentation built on Oct. 11, 2026, 5:07 p.m.