Do_et_al_summary_statistics: Summary statistics from Do et al. (2013)

In budgetIVr: Partial Identification of Causal Effects with Mostly Invalid Instruments

Summary statistics from Do et al. (2013)

Description

Common variants associated with plasma triglycerides and risk for coronary artery disease. Preprocessed and harmonized summary statistics from a Mendelian randomization analysis, including summary statistics for variants' association with plasma triglyceride levels, serum HDL levels, serum LDL levels and risk of coronary artery disease (CAD). Dataset previously applied in the mode-based estimate approach of Hartwig et al. (2017). Each row of the dataset corresponds to a single genetic variant (single nucleotide polymorphism) found to be associated with either the HDL, LDL, or triglyceride biomarkers across a population of 180,000 (HDL, LDL) or 86,000 (triglyceride) individuals. Got further biological and statistical details, see Do et al. (2013).

Usage

data(Do_et_al_summary_statistics)

Format

A data frame with 185 rows and 14 variables:

Details

X

A unique identifier from 1 to 185.

rsID

A unique string specifying each SNP using the rsID format.

chr

String specifying the chromosomal position of each SNP.

a1

Character specifying one allele of the SNP (all 185 SNPs are assumed to be biallelic).

a2

Character specifying the other allele of the SNP.

betaLDL

Effect size (linear regression) for association between SNP allele and LDL.

pLDL

p-value for testing association between SNP allele and LDL.

betaHDL

Effect size (linear regression) for association between SNP allele and HDL.

pHDL

p-value for testing association between SNP allele and HDL.

betaTri

Effect size (linear regression) for association between SNP allele and triglyceride.

pTri

p-value for testing association between SNP allele and triglyceride.

betaCAD

Effect size (logistic regression) for association between SNP allele and CAD.

pCAD

p-value for testing association between SNP allele and CAD.

References

Ron Do et al. (2013). Common variants associated with plasma triglycerides and risk for coronary artery disease. Nat Genet. 45.11, pp. 1345–52.

Fernando Pires Hartwig, George Davey Smith, and Jack Bowden. (2017). Robust inference in summary data Mendelian randomization via the zero modal pleiotropy assumption. Int. J. Epidemiol. 46.6, pp. 1985–1998.

Examples

# Extracting relevant summary statistics to investigate the causal effect of HDL on CAD risk.

data(Do_et_al_summary_statistics)

candidatesHDL = Do_et_al_summary_statistics[Do_et_al_summary_statistics$pHDL <= 1e-8, ]

candidate_labels <- candidatesHDL$rsID
d_Z <- length(candidate_labels)

beta_x <- candidatesHDL$betaHDL

beta_y <- candidatesHDL$betaCAD

SE_beta_y <- abs(beta_y) / qnorm(1-candidatesHDL$pCAD/2)

# For confidence set in budgetIV/budgetIV_scalar.
alpha = 0.05
delta_beta_y <- qnorm(1 - alpha/(2*d_Z))*SE_beta_y

budgetIVr documentation built on April 16, 2025, 5:11 p.m.