孟德尔随机化, Heterogeneity异质性, Q & I2

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# 【 Heterogeneity异质性
#    Cochran's Q test  & I2 】

library(TwoSampleMR)
# 前期准备
exp_data <- extract_instruments(
  outcomes = "ebi-a-GCST009541")
out_data <- extract_outcome_data(
  snps = exp_data$SNP, 
  outcomes = "ieu-b-102") 
dat <- TwoSampleMR::harmonise_data(
  exposure_dat = exp_data,
  outcome_dat = out_data)
dat <- subset(dat,mr_keep)


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# 【底层】meta分析 单个SNP
res_single1 <- mr_singlesnp(dat,all_method = c("mr_ivw"))
# 计算I-squ
library(metafor)
res_single2 <- res_single1[grep("^rs",res_single1$SNP),]
res_meta <-metafor::rma(yi=res_single2$b,   # 填入res的b, 下同
                        sei = res_single2$se,
                        weights = 1/dat$se.outcome^2,
                        data=res_single2,
                        method = 'FE')
res_meta


# 计算 Cochran’sQ
res_hete <- TwoSampleMR::mr_heterogeneity(dat)
res_hete


# # Isquare 计算
library(MendelianRandomization)
MRInputObject <- MendelianRandomization::mr_input(
  bx = dat$beta.exposure,
  bxse = dat$se.exposure,
  by = dat$beta.outcome,
  byse = dat$se.outcome,
  snps = dat$SNP )
#
MendelianRandomization::mr_ivw(
  object = MRInputObject,model = "fixed")


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