Nothing
## -----------------------------------------------------------------------------
library(MendelianRandomization)
## -----------------------------------------------------------------------------
MRInputObject <- mr_input(bx = ldlc,
bxse = ldlcse,
by = chdlodds,
byse = chdloddsse)
MRInputObject # example with uncorrelated variants
MRInputObject.cor <- mr_input(bx = calcium,
bxse = calciumse,
by = fastgluc,
byse = fastglucse,
corr = calc.rho)
MRInputObject.cor # example with correlated variants
## ---- eval=FALSE--------------------------------------------------------------
# MRInputObject <- mr_input(ldlc, ldlcse, chdlodds, chdloddsse)
## -----------------------------------------------------------------------------
IVWObject <- mr_ivw(MRInputObject,
model = "default",
robust = FALSE,
penalized = FALSE,
correl = FALSE,
weights = "simple",
psi = 0,
distribution = "normal",
alpha = 0.05)
IVWObject <- mr_ivw(mr_input(bx = ldlc, bxse = ldlcse,
by = chdlodds, byse = chdloddsse))
IVWObject
IVWObject.correl <- mr_ivw(MRInputObject.cor,
model = "default",
correl = TRUE,
distribution = "normal",
alpha = 0.05)
IVWObject.correl <- mr_ivw(mr_input(bx = calcium, bxse = calciumse,
by = fastgluc, byse = fastglucse, corr = calc.rho))
IVWObject.correl
## -----------------------------------------------------------------------------
WeightedMedianObject <- mr_median(MRInputObject,
weighting = "weighted",
distribution = "normal",
alpha = 0.05,
iterations = 10000,
seed = 314159265)
WeightedMedianObject <- mr_median(mr_input(bx = ldlc, bxse = ldlcse,
by = chdlodds, byse = chdloddsse))
WeightedMedianObject
SimpleMedianObject <- mr_median(mr_input(bx = ldlc, bxse = ldlcse,
by = chdlodds, byse = chdloddsse), weighting = "simple")
SimpleMedianObject
## -----------------------------------------------------------------------------
EggerObject <- mr_egger(MRInputObject,
robust = FALSE,
penalized = FALSE,
correl = FALSE,
distribution = "normal",
alpha = 0.05)
EggerObject <- mr_egger(mr_input(bx = ldlc, bxse = ldlcse,
by = chdlodds, byse = chdloddsse))
EggerObject
EggerObject.corr <- mr_egger(MRInputObject.cor,
correl = TRUE,
distribution = "normal",
alpha = 0.05)
EggerObject.corr <- mr_egger(mr_input(bx = calcium, bxse = calciumse,
by = fastgluc, byse = fastglucse, corr = calc.rho))
EggerObject.corr
## -----------------------------------------------------------------------------
MaxLikObject <- mr_maxlik(MRInputObject,
model = "default",
correl = FALSE,
psi = 0,
distribution = "normal",
alpha = 0.05)
MaxLikObject <- mr_maxlik(mr_input(bx = ldlc, bxse = ldlcse,
by = chdlodds, byse = chdloddsse))
MaxLikObject
MaxLikObject.corr <- mr_maxlik(mr_input(bx = calcium, bxse = calciumse,
by = fastgluc, byse = fastglucse, corr = calc.rho))
MaxLikObject.corr
## -----------------------------------------------------------------------------
MRMVInputObject <- mr_mvinput(bx = cbind(ldlc, hdlc, trig),
bxse = cbind(ldlcse, hdlcse, trigse),
by = chdlodds,
byse = chdloddsse)
MRMVInputObject
## -----------------------------------------------------------------------------
MRMVObject <- mr_mvivw(MRMVInputObject,
model = "default",
correl = FALSE,
distribution = "normal",
alpha = 0.05)
MRMVObject <- mr_mvivw(MRMVInputObject)
MRMVObject
## -----------------------------------------------------------------------------
MBEObject <- mr_mbe(MRInputObject,
weighting = "weighted",
stderror = "delta",
phi = 1,
seed = 314159265,
iterations = 10000,
distribution = "normal",
alpha = 0.05)
MBEObject <- mr_mbe(mr_input(bx = ldlc, bxse = ldlcse,
by = chdlodds, byse = chdloddsse))
MBEObject
## ---- eval = FALSE------------------------------------------------------------
# HetPenObject <- mr_hetpen(MRInputObject,
# prior = 0.5,
# CIMin = -1,
# CIMax = 1,
# CIStep = 0.001,
# alpha = 0.05)
## -----------------------------------------------------------------------------
HetPenObject <- mr_hetpen(mr_input(bx = ldlc[1:10], bxse = ldlcse[1:10],
by = chdlodds[1:10], byse = chdloddsse[1:10]), CIMin = -1, CIMax = 5, CIStep = 0.01)
HetPenObject
## -----------------------------------------------------------------------------
bcrp =c(0.160, 0.236, 0.149, 0.09, 0.079, 0.072, 0.047, 0.069)
bcrpse =c(0.006, 0.009, 0.006, 0.005, 0.005, 0.005, 0.006, 0.011)
bchd =c(0.0237903, -0.1121942, -0.0711906, -0.030848, 0.0479207, 0.0238895,
0.005528, 0.0214852)
bchdse =c(0.0149064, 0.0303084, 0.0150552, 0.0148339, 0.0143077, 0.0145478,
0.0160765, 0.0255237)
HetPenObject.multimode <- mr_hetpen(mr_input(bx = bcrp, bxse = bcrpse,
by = bchd, byse = bchdse))
HetPenObject.multimode
## -----------------------------------------------------------------------------
MRInputObject <- mr_input(bx = ldlc,
bxse = ldlcse,
by = chdlodds,
byse = chdloddsse)
MRAllObject_all <- mr_allmethods(MRInputObject, method = "all")
MRAllObject_all
MRAllObject_egger <- mr_allmethods(MRInputObject, method = "egger")
MRAllObject_egger
MRAllObject_main <- mr_allmethods(MRInputObject, method = "main")
MRAllObject_main
## ---- eval = FALSE------------------------------------------------------------
# mr_plot(mr_input(bx = ldlc, bxse = ldlcse, by = chdlodds, byse = chdloddsse),
# error = TRUE, orientate = FALSE, line = "ivw")
## -----------------------------------------------------------------------------
mr_plot(mr_input(bx = ldlc, bxse = ldlcse, by = chdlodds, byse = chdloddsse),
error = TRUE, orientate = FALSE, line = "ivw", interactive = FALSE)
## -----------------------------------------------------------------------------
mr_plot(mr_input(bx = ldlc, bxse = ldlcse, by = chdlodds, byse = chdloddsse),
error = TRUE, orientate = FALSE, line = "ivw", interactive = FALSE, labels = TRUE)
## -----------------------------------------------------------------------------
mr_plot(MRAllObject_all)
## -----------------------------------------------------------------------------
mr_plot(MRAllObject_egger)
## -----------------------------------------------------------------------------
mr_plot(mr_allmethods(mr_input(bx = hdlc, bxse = hdlcse,
by = chdlodds, byse = chdloddsse)))
## -----------------------------------------------------------------------------
path.noproxy <- system.file("extdata", "vitD_snps_PhenoScanner.csv",
package = "MendelianRandomization")
path.proxies <- system.file("extdata", "vitD_snps_PhenoScanner_proxies.csv",
package = "MendelianRandomization")
extract.pheno.csv(
exposure = "log(eGFR creatinine)", pmidE = 26831199, ancestryE = "European",
outcome = "Tanner stage", pmidO = 24770850, ancestryO = "European",
file = path.noproxy)
extract.pheno.csv(
exposure = "log(eGFR creatinine)", pmidE = 26831199, ancestryE = "European",
outcome = "Tanner stage", pmidO = 24770850, ancestryO = "European",
rsq.proxy = 0.6,
file = path.proxies)
extract.pheno.csv(
exposure = "log(eGFR creatinine)", pmidE = 26831199, ancestryE = "European",
outcome = "Asthma", pmidO = 20860503, ancestryO = "European",
rsq.proxy = 0.6,
file = path.proxies)
Any scripts or data that you put into this service are public.
Add the following code to your website.
For more information on customizing the embed code, read Embedding Snippets.