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yoonsucho / CAMERA

Mendelian Randomization approach using Cross Ancestral Model
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List of studies to analyse #15

Open explodecomputer opened 2 years ago

explodecomputer commented 2 years ago 
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

Smoking initiation

Smoking cigarettes per day

LDL

SBP

Outcomes

CAD

T2D

eGFR

Schizophrenia

Lung cancer

Breast cancer

Colorectal cancer

Aspartate aminotransferase

SBP

Asthma (GBMI)

COPD (GBMI)

Heart failure (GBMI)

Stroke (GBMI)

yoonsucho commented 2 years ago

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