List of studies to analyse

[explodecomputer]

library(readxl)
library(dplyr)
library(ggplot2)

d <- readxl::read_xlsx("~/Downloads/sem_bmi_results_210422.xlsx", sheet="scaling-updatedR")

d <- subset(d, Methods=="maxz")
mod1 <- dplyr::select(d, Exposure, Outcome, nsnp, bivhat, se, pval, aic=aic_model1) %>% mutate(model="combined")
mod2 <- dplyr::select(d, Exposure, Outcome, nsnp, bivhat=bivhat_EUR, se=se_EUR, pval=pval_EUR, aic=aic_model2) %>% mutate(model="EUR")
mod3 <- dplyr::select(d, Exposure, Outcome, nsnp, bivhat=bivhat_EAS, se=se_EAS, pval=pval_EAS, aic=aic_model2) %>% mutate(model="EAS")
mod <- bind_rows(mod1, mod2, mod3)

ggplot(mod %>% filter(! Outcome %in% c("Arrythmia", "Glucoma", "Asthma", "T2D"), aes(x=bivhat, y=model)) +
geom_point(aes(colour=model)) +
geom_errorbarh(aes(colour=model, xmin=bivhat - se * 1.96, xmax=bivhat + se * 1.96), height=0) +
facet_grid(Outcome ~ Exposure, scale="free_x") +
geom_vline(xintercept=0, linetype="dotted")

Exposures

BMI

• bbj-a-1 (EAS)
• ieu-b-40 (EUR)

Smoking initiation

• ieu-b-4877 (EUR)
• bbj-a-78 (EAS)

Smoking cigarettes per day

• ieu-b-25 (EUR)
• ieu-b-5071 (EAS)

LDL

• ieu-b-110 (EUR)
• bbj-a-31 (EAS)

SBP

• bbj-a-52 (EAS)
• ukb-b-20175 (EUR)

Outcomes

CAD

• ebi-a-GCST005195 (EUR)
• bbj-a-159 (EAS)

T2D

• ebi-a-GCST007515 (EUR)
• ebi-a-GCST010118 (EAS)

eGFR

• bbj-a-60 (EAS)
• ieu-b-4832 (EUR)

Schizophrenia

• ieu-b-42 (EUR)
• ieu-b-5070 (EAS)

Lung cancer

• ieu-a-966 (EUR)
• bbj-a-133 (EAS)

Breast cancer

• ieu-a-1126 (EUR)
• bbj-a-160 (EAS)

Colorectal cancer

• ieu-b-4965 (EUR)
• bbj-a-107 (EAS)

Aspartate aminotransferase

• ukb-d-30650_irnt (EUR)
• bbj-a-8 (EAS)

SBP

• bbj-a-52 (EAS)
• ieu-b-38 (EUR)

Asthma (GBMI)

COPD (GBMI)

Heart failure (GBMI)

Stroke (GBMI)

[yoonsucho]

T2D for EUR is changed to ebi-a-GCST007515 as the ebi-a-GCST006867 includes some South Asians
Continuous traits from BBJ GWAS might not be suitable for this model as they adjusted for 47 diseases