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# 【 Heterogeneity異質(zhì)性
#? ? Cochran's Q test? & I2 】

library(TwoSampleMR)
# 前期準(zhǔn)備
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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# 【底層】meta分析 單個SNP
res_single1 <- mr_singlesnp(dat,all_method = c("mr_ivw"))
# 計算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


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


# # Isquare 計算
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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