causal-genomics-mendelian-randomization

name	causal-genomics-mendelian-randomization
description	Estimate causal effects of an exposure on an outcome from GWAS summary statistics using genetic instruments. Implements IVW (fixed/random), MR-Egger, weighted median/mode, MR-RAPS, CAUSE, GSMR-HEIDI, MR-PRESSO, MVMR, MR-Clust, LCV, and LHC-MR via TwoSampleMR, MendelianRandomization, MR-PRESSO, cause, and lhcMR. Use when testing causal direction between traits, evaluating drug-target effects via cis-pQTL/cis-eQTL, performing multivariable mediation MR, distinguishing causation from correlated horizontal pleiotropy, or producing STROBE-MR-compliant sensitivity batteries.
tool_type	mixed
primary_tool	TwoSampleMR

Version Compatibility

Reference examples tested with: TwoSampleMR 0.6.0+, MendelianRandomization 0.10+, MR-PRESSO 1.0+, cause 1.2+, MVMR 0.4+, ieugwasr 1.0+, MRlap 0.0.3.2+, coloc 5.2+, mrclust 0.1+, lhcMR 0.0.1+, R 4.4+. Both TwoSampleMR 0.6.0 and ieugwasr 1.0 are the JWT-transition versions; older versions still expect deprecated OAuth.

Before using code patterns, verify installed versions match. If versions differ:

• R: packageVersion('<pkg>') then ?function_name to verify parameters
• CLI (plink, GCTA-GSMR): <tool> --version then <tool> --help

If code throws an error referencing a function that has moved (e.g. ieugwasr::ld_clump vs TwoSampleMR::clump_data) or an OAuth token failure, introspect the installed API and adapt the example rather than retrying.

Mendelian Randomization

"Test whether trait X causally affects trait Y from GWAS summary statistics" -> Use genetic variants as instrumental variables (IVs) that satisfy three assumptions (relevance, independence, exclusion restriction) to estimate beta_causal = beta_outcome / beta_exposure under the IV framework (Davey Smith & Ebrahim 2003 IJE 32:1; Burgess Thompson 2017 SAGE textbook). Tool choice is a decision about the regime (one-sample vs two-sample, sparse vs polygenic, drug-target vs polygenic exposure) and the pleiotropy model (balanced, directional InSIDE, correlated horizontal). Wrong tool inflates Type-I error or attenuates true effects in a direction predictable from the bias structure.

• R: TwoSampleMR::mr() orchestrates IVW + Egger + weighted median + weighted mode in one call
• R: MendelianRandomization::mr_ivw / mr_egger / mr_median / mr_mbe / mr_conmix per-method API (S4 objects; MR-RAPS is NOT in this package -- use TwoSampleMR::mr_raps() which wraps the GitHub mr.raps)
• R: MRPRESSO::mr_presso() global / outlier / distortion tests
• R: cause::cause() correlated horizontal pleiotropy mixture
• R: MVMR::strength_mvmr() + MVMR::ivw_mvmr() multivariable conditional-F + IVW

Statistical Model Taxonomy

Method	Pleiotropy assumption	Min instruments	Strength	Fails when
IVW (fixed)	All IVs valid	2	Most efficient under no pleiotropy	Any directional or balanced pleiotropy inflates Type-I
IVW (random effects)	Balanced + InSIDE	3	Standard primary; absorbs heterogeneity into wider SE	Directional pleiotropy biases the point estimate
MR-Egger	Directional pleiotropy + InSIDE	10+ for power	Detects + corrects directional pleiotropy via intercept (Bowden 2015 IJE 44:512)	NOME violated (I^2_GX < 0.9); SIMEX correction required; underpowered <10 SNPs
Weighted median	Up to 50% invalid IVs	3	Robust to a minority of bad instruments (Bowden 2016 Genet Epidemiol 40:304)	>50% invalid IVs
Weighted mode	Zero modal pleiotropy (ZEMPA)	3	Robust if the modal estimate is unbiased (Hartwig 2017 IJE 46:1985)	Bimodal pleiotropy; small numbers
MR-RAPS	Balanced pleiotropy + weak instruments	10+	Profile-score robust to weak-IV + balanced horizontal pleiotropy (Zhao 2020 Ann Stat 48:1742)	Strong directional pleiotropy; CRAN-archived 2025-03-01
CAUSE	Correlated horizontal pleiotropy (CHP)	100+ sig SNPs	Explicit shared-factor mixture; protects against CHP-driven false positives (Morrison 2020 Nat Genet 52:740)	Sparse polygenic exposures; <100 sig SNPs
GSMR + HEIDI-outlier	Outlier removal under InSIDE	10+	Alternative outlier detection; integrates with LD reference (Zhu 2018 Nat Commun 9:224)	Requires individual-level LD; HEIDI conservative
MR-PRESSO	Outlier-driven horizontal pleiotropy	4+	Global / outlier / distortion three-step (Verbanck 2018 Nat Genet 50:693)	Blind to CHP; computationally heavy at large NbDistribution
MVMR (IVW)	Conditional independence after measured pleiotropy	1+ per exposure	Accounts for measured horizontal pleiotropy via multivariable regression (Sanderson 2019 IJE 48:713)	Conditional F < 10 on any exposure
MR-Clust	Heterogeneous causal effects (multiple mechanisms)	30+	Clusters SNPs by their causal-effect estimate (Foley 2020 Bioinformatics 37:531)	Single causal mechanism; small instrument sets
Contamination mixture	Mixture of valid + invalid IVs	10+	Profile-likelihood mixture (Burgess 2020 Nat Commun 11:376)	Sparse signal
LCV	Genome-wide; distinguishes causation vs genetic correlation	All SNPs	Tests gcp parameter using LDSC-style block jackknife (O'Connor & Price 2018 Nat Genet 50:1728)	Two-trait covariance dominated by a third confounder
LHC-MR	Bidirectional + heritable confounder	All SNPs	Joint likelihood over genome-wide markers; estimates both directions + confounder (Darrous 2021 Nat Commun 12:7274)	Computationally heavy; rare-variant trait
MRlap	Sample overlap + winner's curse + weak-IV jointly	Genome-wide sumstats	LDSC-scaffolded joint correction (Mounier & Kutalik 2023 Genet Epidemiol 47:314)	LDSC intercept poorly estimated (h^2 < 0.05); non-EUR without matched LD scores
Doubly-Ranked MR (DRMR)	Non-linear, non-parametric	5+ strata	Non-parametric stratification (Tian 2023 PLoS Genet 19:e1010823); replaces residual stratification when linearity fails	Continuous exposures only; needs individual-level data; Hamilton 2023 medRxiv 23293658 shows stratum-specific bias from age/sex

Methodology evolves; benchmark consensus shifts every 2-3 years. Verify against the current Slob & Burgess 2020 Genet Epidemiol, Burgess 2023 Wellcome Open Res "Guidelines for performing Mendelian randomization" (v3+), and STROBE-MR 2021 reporting standards before locking a method as primary.

Decision Tree by Experimental Scenario

Scenario	Primary method	Sensitivity battery	Why
Standard two-sample, independent cohorts, polygenic exposure	IVW (random)	Egger + weighted median + MR-PRESSO + MR-RAPS + Steiger	Default; covers balanced, directional, outlier, weak-IV regimes
One-sample (e.g. UK Biobank both ends)	IVW with weak-IV-aware (MR-RAPS)	Egger + LCV + jackknife SE	One-sample bias formulas: Bowden 2019 IJE 48:728; F-stat floor shifts to F >= 20; jackknife SE preferred over analytic at one-sample scale; do NOT run exposure GWAS and outcome GWAS on the same individuals then claim two-sample (Hartwig 2021 collider bias); within-stratum MR (e.g. "MR among smokers") risks collider bias from the stratification variable
Partial sample overlap (UKB exposure + UKB outcome)	MR-RAPS with overlap correction	Sample-overlap-adjusted IVW (Burgess 2016 Genet Epidemiol 40:597)	Bias is intermediate, proportional to z-score correlation
Drug-target / cis-MR (cis-pQTL, cis-eQTL)	IVW restricted to cis window	Colocalization PP.H4 + LD-prune within window	Exclusion restriction relaxed because the protein/transcript directly mediates effect (Schmidt 2020 Nat Commun 11:3255)
MVMR for measured pleiotropy (e.g. LDL adjusted for HDL/TG)	MVMR::ivw_mvmr	Conditional F + Q_A heterogeneity	Required when exposures correlate via shared SNPs
Mediation MR (X -> M -> Y)	MVMR difference of total vs direct	Two-step MR + product-of-coefficients (Carter 2021 Eur J Epidemiol 36:465)	Network MR; quantifies indirect effect
Polygenic exposure with potential CHP (e.g. BMI -> CHD)	CAUSE (primary) + IVW (secondary)	Egger + MR-PRESSO + LCV	CAUSE explicitly models CHP via shared-factor; needs >=100 sig SNPs
Binary outcome (e.g. T2D) on linear scale	IVW on log-OR with log-additive coding	All sensitivity on log-OR; report exp(beta)	Linearity of MR estimating equation holds on log-OR not OR
Time-to-event (Cox) outcome	IVW on log-HR	Burgess & Labrecque 2018 Eur J Epidemiol 33:947 framework	Non-collapsibility caveats apply
Non-linear MR (e.g. alcohol J-curve)	DRMR (Tian 2023) + residual stratification side-by-side	Negative-control outcomes (genotype-vs-sex within strata); Hamilton 2023 limitation cited	Both methods produce stratum-specific bias from age/sex effects (Hamilton 2023 medRxiv 23293658); pre-specify the non-linear hypothesis, do not data-snoop the J-curve, report negative-control sanity checks
Single-patient rare disease	Not MR -- use FRASER/DROP outlier framework	See alternative-splicing/outlier-splicing-detection	MR requires summary stats; n=1 is wrong regime

One-Sample vs Two-Sample Bias Direction

Design	Weak-IV bias direction	Reason
One-sample, F<10	Toward confounded observational estimate (overestimates causal effect if confounding is in same direction)	Sample correlation between IV-X and IV-Y residuals
Two-sample non-overlapping, F<10	Toward null	Independent samples decouple residuals (Burgess 2011 IJE 40:755)
Two-sample with partial overlap	Intermediate; proportional to overlap fraction and z-score correlation	Burgess 2016 Genet Epidemiol 40:597; correction available

Operational rule: Whenever both GWAS came from UK Biobank (or any single biobank), treat the analysis as one-sample-equivalent and prefer MR-RAPS as primary. Treating it as "two-sample because separate GWAS files" is a common error and produces overestimates.

MRlap: unified correction for sample overlap + winner's curse + weak instruments

MRlap (Mounier & Kutalik 2023 Genet Epidemiol 47:314) jointly corrects three biases that previously required three separate tools: sample overlap, winner's curse, and weak-instrument bias. It builds on an LDSC scaffold (cross-trait LD-score regression intercept estimates the overlap-induced covariance) and reweights the IVW estimate against the analytical bias-correction formula.

remotes::install_github('n-mounier/MRlap')   # never on CRAN; bioconductor unsuitable
library(MRlap)

fit <- MRlap(
    exposure = gwas_X_df, exposure_name = 'BMI',
    outcome = gwas_Y_df, outcome_name = 'T2D',
    ld = 'eur_w_ld_chr/', hm3 = 'w_hm3.snplist',   # LDSC reference files
    MR_threshold = 5e-8, MR_pruning_dist = 500, MR_pruning_LD = 0.05
)
fit$MRcorrection$corrected_effect       # overlap + winner's curse + weak-IV corrected
fit$MRcorrection$corrected_effect_se
fit$LDSC$h2_LDSC                         # heritability sanity check
fit$LDSC$lambda                          # sample-overlap-induced lambda; ~0 means no overlap

Decision rule -- prefer MRlap when: (a) any sample overlap is suspected, (b) only sumstats are available (no individual-level data for re-running GWAS on disjoint samples), (c) exposure discovery and outcome were both run inside the same biobank (UKB-on-UKB, FinnGen-on-FinnGen). MRlap returns NA / unstable estimates when h^2 < 0.05; in that regime, fall back to Burgess 2016 overlap-corrected IVW plus MR-RAPS for the weak-IV component.

Drug-Target / cis-MR Framework

cis-MR restricts instruments to the cis-regulatory window of the gene encoding the protein/transcript exposure (Schmidt 2020 Nat Commun 11:3255), relaxing the exclusion-restriction assumption because the protein product directly mediates the SNP's effect on the outcome. Operational core: extract cis-pQTL/cis-eQTL within +/-500 kb of the gene; clump at r2 < 0.1 (looser than polygenic MR to retain power within a narrow window); require colocalization PP.H4 >= 0.7; flag protein-altering variants (PAV) which can break SomaScan/Olink aptamer/antibody binding rather than reflect biology.

Full drug-target cis-MR workflow including UKB-PPP / deCODE / Fenland pQTL panels, PAV flagging, Olink vs SomaScan replication (~15-30% cross-platform disagreement), and the operational claim ladder lives in causal-genomics/proteome-mr-drug-target. Use that skill for any drug-target nomination.

Binary outcomes and non-collapsibility

MR with logistic-GWAS sumstats returns per-allele log-OR on the population-averaged (marginal) scale, NOT the conditional log-OR (Burgess & Labrecque 2018 Eur J Epidemiol 33:947; Burgess 2017 Stat Methods Med Res 26:2333). For rare disease (prevalence < 10%), OR ~= RR ~= HR and the distinction is harmless. For common disease, OR diverges from RR/HR and the MR estimate cannot be back-converted to a conditional effect without strong assumptions; report as "per 1-SD increase in genetically-predicted X, OR for Y = ..." rather than implying an individual-level intervention effect.

Collider bias in case-only or disease-progression cohorts (Hu 2022 IJE 51:1289): conditioning the outcome on disease status (e.g. studying progression among diabetics) opens a collider path between any cause of disease and any cause of progression. MR within affected subsets without explicit adjustment for selection probability is fragile; weight by inverse probability of selection or restrict claims to the unconditioned population.

Per-Method Failure Modes

IVW under directional pleiotropy

Trigger: Several SNPs affect the outcome through pathways not via the exposure, in a consistent direction.

Mechanism: IVW is a weighted regression through origin; non-zero mean pleiotropy shifts the slope.

Symptom: Egger intercept p < 0.05 with non-zero estimate; IVW differs from weighted median; MR-PRESSO global test p < 0.05.

Fix: Use Egger (if I^2_GX >= 0.9 -- otherwise SIMEX-correct via the simex package applied to the Egger fit, treating se.exposure as measurement error in beta.exposure); cross-check with weighted median, MR-PRESSO, and CAUSE; report IVW only as one of a panel, never alone. The MendelianRandomization::mr_egger() function accepts distribution='normal' and reports NOME-corrected estimates internally but does NOT expose a SIMEX wrapper.

Weak-instrument bias direction

Trigger: Mean per-instrument F-statistic < 10, or several individual F < 10.

Mechanism: Weak IVs amplify finite-sample correlation between IV-X and IV-Y errors; bias direction depends on overlap regime (see table above).

Symptom: Estimates shift markedly when removing the weakest instruments; one-sample MR estimates much larger than two-sample.

Fix: Compute F per instrument from the EXPOSURE GWAS, not the outcome; exclude F < 10; use MR-RAPS (handles weak IVs by design); for two-sample, also report unweighted IVW (less weak-IV-bias-inflated than weighted in some regimes).

Winner's curse at P~5e-8

Trigger: Discovery GWAS is the source of both instrument selection and effect-size estimates.

Mechanism: SNPs that just cross 5e-8 in discovery have over-estimated effect sizes (regression toward the mean in independent replication); MR uses inflated beta_X, biasing causal estimate.

Symptom: MR effect shrinks substantially when using effect sizes from an independent replication GWAS.

Fix: (1) Three-sample design (discovery / replication-for-instrument-effect / outcome) where feasible. (2) When sumstats-only: MRlap (Mounier 2023), MR-SimSS (sample-splitting from sumstats), or RIVW (Ma 2023 JASA -- rerandomized IVW) jointly correct winner's curse + weak IVs + overlap. (3) Sadreev 2024 IJE 52:1209 empirical magnitude: 5-15% bias inflation at p < 5e-8; larger at relaxed thresholds.

NOME violation invalidating Egger

Trigger: Running MR-Egger with I^2_GX < 0.9.

Mechanism: Egger assumes NO Measurement Error in exposure effect sizes (NOME); when violated, Egger slope is attenuated toward null with reciprocal bias on the intercept.

Symptom: mr_pleiotropy_test() Egger estimate disagrees with weighted median in magnitude but agrees in direction; Isq() function returns <0.9.

Fix: Compute Isq(beta_X, se_X) (Bowden 2016 IJE 45:1961); if <0.9, apply SIMEX correction via simex package or report Egger as exploratory only. The MendelianRandomization package's mr_egger() returns a NOME-aware corrected estimate.

Steiger filter false flag under unmeasured confounding

Trigger: Applying steiger_filtering() on traits with unmeasured shared confounders (e.g. SES).

Mechanism: Steiger compares variance explained in exposure vs outcome per SNP; an unmeasured confounder upstream of both produces SNPs that explain more variance in the outcome than the exposure, falsely flagging "reverse causation" (Hemani Tilling 2022 Wellcome Open Res 7:14).

Symptom: Many SNPs flagged as wrong-direction yet biology and prior MR support forward causation.

Fix: Treat Steiger as a heuristic, not gospel; cross-validate direction with bidirectional MR (forward + reverse with independent instrument sets); for known-confounder-rich domains (psychiatric traits, SES proxies) use LCV or LHC-MR instead, which jointly model confounders.

Palindromic SNP harmonization

Trigger: SNPs with alleles A/T or C/G near MAF 0.5.

Mechanism: Strand orientation is ambiguous for palindromic SNPs when allele frequencies are intermediate; flipping introduces sign errors that look like pleiotropy.

Symptom: harmonise_data() reports many palindromic SNPs dropped; remaining SNPs show heterogeneity from a handful.

Fix: Default action = 2 (infer from allele frequencies) drops MAF~0.5 palindromes; action = 3 drops ALL palindromes (most conservative); never use action = 1 (assumes forward strand) unless both GWAS are guaranteed to use the same strand convention. Document choice in methods.

Quantitative Thresholds

Threshold	Source	Rationale
F-statistic > 10 per instrument	Staiger & Stock 1997 (linear IV)	Heuristic; debated (Burgess 2011 IJE; Zhao 2020 argues 10 is too low for one-sample)
Conditional F > 10 per exposure (MVMR)	Sanderson 2019 IJE 48:713	Total F can be high while conditional F low; per-exposure F is what matters
I^2_GX >= 0.9 for Egger	Bowden 2016 IJE 45:1961	NOME assumption; below this, SIMEX correction required
CAUSE >= 100 significant SNPs	Morrison 2020 Nat Genet 52:740	Mixture model needs signal density for shared-factor estimation
Egger >= 10 instruments	Bowden 2015 IJE 44:512	Power for slope test in weighted regression
Sample-overlap z-score correlation	Burgess 2016 Genet Epidemiol 40:597	Use LDSC bivariate intercept as proxy; correct IVW SE accordingly
Clumping r2 < 0.001, 10 Mb window	TwoSampleMR default; matches GWAS LD norms	Polygenic MR; cis-MR uses r2 < 0.1 within window
Steiger p < 0.05	Hemani 2017 PLoS Genet 13:e1007081	Heuristic; subject to confounder caveat (Hemani Tilling 2022)
MR-PRESSO NbDistribution	1000 exploratory; >= 5000 publication; >= 10000 stringent	Verbanck 2018 Nat Genet 50:693; precision of global p-value scales with NbDistribution
STROBE-MR all 20 items	Skrivankova 2021 JAMA 326:1614; BMJ 375:n2233	Required since 2022 by most epidemiology journals
Bonferroni for pheWAS-MR	Standard	Many outcomes; FDR if exploratory

TwoSampleMR Standard Workflow

Goal: Produce a defensible primary IVW estimate plus a full sensitivity battery from two-sample summary statistics.

Approach: Extract genome-wide significant instruments -> clump (local plink preferred) -> extract outcome -> harmonise -> mr -> pleiotropy + heterogeneity + leave-one-out -> Steiger -> MR-PRESSO -> report.

library(TwoSampleMR)
library(ieugwasr)

exposure_raw <- read_exposure_data(
    filename = 'exposure_gwas.tsv', sep = '\t',
    snp_col = 'SNP', beta_col = 'BETA', se_col = 'SE',
    effect_allele_col = 'A1', other_allele_col = 'A2',
    eaf_col = 'EAF', pval_col = 'P'
)

exposure_sig <- subset(exposure_raw, pval.exposure < 5e-08)  # genome-wide significance

# F-statistic computed from EXPOSURE (Burgess 2011); ratio of squared effect to its variance
exposure_sig$f_stat <- (exposure_sig$beta.exposure / exposure_sig$se.exposure)^2
exposure_sig <- subset(exposure_sig, f_stat >= 10)  # Staiger-Stock 1997 weak-IV heuristic

clumped <- ld_clump(
    data.frame(rsid = exposure_sig$SNP, pval = exposure_sig$pval.exposure),
    clump_r2 = 0.001, clump_kb = 10000,  # polygenic MR convention
    plink_bin = genetics.binaRies::get_plink_binary(),
    bfile = '1kg_EUR/EUR'
)
exposure_dat <- subset(exposure_sig, SNP %in% clumped$rsid)

outcome_dat <- read_outcome_data(
    filename = 'outcome_gwas.tsv', snps = exposure_dat$SNP, sep = '\t',
    snp_col = 'SNP', beta_col = 'BETA', se_col = 'SE',
    effect_allele_col = 'A1', other_allele_col = 'A2',
    eaf_col = 'EAF', pval_col = 'P'
)

dat <- harmonise_data(exposure_dat, outcome_dat, action = 2)  # infer from EAF; drops MAF~0.5 palindromes

primary <- mr(dat, method_list = c('mr_ivw', 'mr_egger_regression',
                                    'mr_weighted_median', 'mr_weighted_mode'))

heterogeneity <- mr_heterogeneity(dat)         # Cochran Q
pleiotropy <- mr_pleiotropy_test(dat)          # Egger intercept
loo <- mr_leaveoneout(dat)                     # influential-SNP check
steiger <- directionality_test(dat)            # variance-explained direction

MR-PRESSO Outlier Detection

Goal: Detect horizontal-pleiotropy outliers, remove them, and test whether the corrected estimate differs from the uncorrected one (distortion test).

Approach: Three-step framework: global test (presence of pleiotropy), outlier test (per-SNP), distortion test (effect change after outlier removal).

library(MRPRESSO)

presso <- mr_presso(
    BetaOutcome = 'beta.outcome', BetaExposure = 'beta.exposure',
    SdOutcome = 'se.outcome', SdExposure = 'se.exposure',
    OUTLIERtest = TRUE, DISTORTIONtest = TRUE,
    data = dat, NbDistribution = 10000,  # >= 10000 for publication-grade p-value precision
    SignifThreshold = 0.05
)

print(presso$`MR-PRESSO results`$`Global Test`)         # any pleiotropy
print(presso$`MR-PRESSO results`$`Distortion Test`)     # change after outlier removal
outlier_snps <- which(presso$`MR-PRESSO results`$`Outlier Test`$Pvalue < 0.05 / nrow(dat))

CAUSE for Correlated Horizontal Pleiotropy

CAUSE (Morrison 2020 Nat Genet 52:740) fits a shared-factor mixture to genome-wide sumstats and compares causal vs sharing-only models by delta-ELPD. Workflow: gwas_merge() -> sample ~1M variants for est_cause_params() -> filter sig SNPs (P < 1e-3) and optionally LD-prune -> cause(X, variants, param_ests). Needs >= 100 sig SNPs. Full annotated example and ELPD interpretation in causal-genomics/pleiotropy-detection.

MVMR with Conditional F

Goal: Estimate the causal effect of exposure X1 on Y, adjusting for measured pleiotropy via X2.

Approach: Format exposures + outcome into MVMR object; compute conditional F per exposure (>10 required); run multivariable IVW; report Q_A heterogeneity.

library(MVMR)

mvmr_dat <- format_mvmr(
    BXGs = cbind(dat$beta.x1, dat$beta.x2),
    BYG = dat$beta.y,
    seBXGs = cbind(dat$se.x1, dat$se.x2),
    seBYG = dat$se.y,
    RSID = dat$SNP
)

condF <- strength_mvmr(r_input = mvmr_dat, gencov = 0)  # per-exposure conditional F
# condF must be > 10 for EACH exposure (Sanderson 2019); total F is misleading

mv_ivw <- ivw_mvmr(r_input = mvmr_dat)
mv_qa <- qhet_mvmr(r_input = mvmr_dat, pcor = 0)  # Q_A heterogeneity

gencov = 0 is valid ONLY if the exposure GWAS samples don't overlap; for overlapping exposures use the bivariate LDSC intercept matrix as gencov. If any conditional F < 10, the IVW point estimate is weak-IV-biased; switch to the Q-minimization estimator: qhet_mvmr(r_input, pcor, CI = TRUE, iterations = 1000) (Sanderson 2021 Stat Med 40:5434), which minimizes Q-statistic heterogeneity rather than weighting by inverse variance and is robust to weak conditional instruments.

Bidirectional and Steiger

exposure_rev <- format_data(outcome_raw, type = 'exposure')  # treat former outcome as exposure
outcome_rev <- format_data(exposure_raw, type = 'outcome')
dat_rev <- harmonise_data(exposure_rev, outcome_rev, action = 2)
results_rev <- mr(dat_rev, method_list = 'mr_ivw')

dat_filt <- steiger_filtering(dat)  # per-SNP; flags SNPs where variance(Y) > variance(X)
dir_test <- directionality_test(dat) # global; correct_causal_direction == TRUE if forward

Report direction operationally: forward p < 5e-8 with reverse p > 0.05; directionality_test() correct_causal_direction == TRUE with Steiger p < 0.05; point estimate in reverse direction has |effect| substantially smaller than forward (reflecting reverse-instrument-strength asymmetry). Example sentence: "Forward MR showed BMI -> T2D (IVW beta = 0.85, p = 2e-15); reverse MR was null (IVW beta = 0.02, p = 0.61); Steiger directionality test favored the forward direction (p = 3e-7)."

Reconciliation: When Methods Disagree

Pattern	Likely cause	Action
IVW sig, Egger null with non-zero intercept	Directional pleiotropy	Report Egger as primary if I^2_GX >= 0.9; otherwise SIMEX-correct
IVW sig, weighted median sig, mode null	Mode underpowered or bimodal pleiotropy	Trust the agreement of IVW + median
MR-PRESSO distortion test sig	Outliers materially shift estimate	Report PRESSO-adjusted estimate as primary
CAUSE sig, IVW sig, same direction	High-confidence causal claim	Report both; emphasize CAUSE rules out CHP
CAUSE null, IVW sig, same direction	CHP indistinguishable from causation	Downgrade to "consistent with causation but not separable from CHP"
Forward MR sig, reverse MR also sig	Bidirectional causation OR confounded	Use LHC-MR or LCV for genome-wide resolution
IVW sig but mean F << 10 in one-sample design	Weak-IV bias toward observational	Re-run with MR-RAPS; report adjusted estimate

Operational rule for publication: Primary IVW + concordant Egger (or weighted median if NOME violated) + non-significant MR-PRESSO global test + Steiger correct direction = publication-ready evidence. CAUSE concordance is required when the exposure is polygenic and the prior on CHP is high (e.g. BMI -> outcome, lipids -> outcome). Single-method "significant IVW" claims should be downgraded to exploratory.

Cohort Gotchas

• UKB GWAS commonly include non-EUR participants; pan-UKB EUR/AFR/EAS/SAS subsets are separate releases. Mixing ancestries inflates instrument strength via population stratification rather than biology.
• FinnGen DF12 (2024) cohort: Finnish founder effects produce narrower LD blocks and higher winner's curse magnitude than UKB at matched sample size.
• MVP / GBMI / AoU: multi-ancestry meta-analyses; stratify by ancestry before MR or use ancestry-specific subsets.
• UKB-on-UKB MR creates one-sample-equivalent bias regardless of "different GWAS file" appearance; use MRlap or move the outcome to an external cohort (FinnGen, BBJ, MVP).

Anticipated Reviewer Pushback

Pushback	Standard response
"Sample overlap between exposure and outcome GWAS?"	LDSC bivariate intercept reported; MRlap or sample-overlap-corrected IVW applied; document overlap fraction
"Weak instruments (F < 10)?"	F computed from EXPOSURE; per-instrument and mean F reported; MR-RAPS used as sensitivity if mean F borderline
"Horizontal pleiotropy?"	IVW + Egger + weighted median + weighted mode + MR-PRESSO; if rg > 0.3 also CAUSE (see pleiotropy-detection)
"Reverse causation?"	Steiger filter applied; bidirectional MR ran; LCV gcp reported if rg > 0.3
"Pre-registered?"	OSF protocol filed; STROBE-MR all 20 items reported
"InSIDE assumption?"	INstrument Strength Independent of Direct Effect -- pleiotropic effects alpha uncorrelated with instrument-exposure effects gamma. Tested via Egger intercept + CHP-aware sensitivity (CAUSE)

Common Errors

Error / symptom	Cause	Solution
F-statistic computed from outcome	Reading off beta.outcome / se.outcome	Compute from EXPOSURE; outcome F is meaningless for IV strength
All instruments dropped at harmonise	All SNPs palindromic; or allele coding mismatch	Verify A1/A2 conventions match; try action = 3 to drop, not assume
Unauthorized / 403 from OpenGWAS	OAuth deprecated May 2024; JWT token required	Generate at api.opengwas.io -> set OPENGWAS_JWT=<token> in ~/.Renviron -> restart R -> verify with ieugwasr::get_opengwas_jwt(). For production, skip the API: use ld_clump_local() with local 1KG bfile (saves rate-limit + auth headaches).
Conditional F vs total F confusion in MVMR	Reporting mean(F) not strength_mvmr() per-exposure	Always use MVMR::strength_mvmr() and report each column
install.packages("mr.raps") fails	CRAN-archived 2025-03-01	remotes::install_github('qingyuanzhao/mr.raps'); TwoSampleMR's mr_raps() wrapper internally calls this package
MR-PRESSO returns NA p-value	NbDistribution too small; signal too thin	Increase to >= 10000; check that >= 4 SNPs remain after harmonization
Egger intercept "highly significant" with 5 SNPs	Underpowered Egger over-fits the slope	Egger needs >= 10 SNPs; below that, intercept is unreliable
Sample-overlap correction ignored	Treating UKB-on-UKB as two-sample	Apply Burgess 2016 correction; or use MR-RAPS
cause() runs forever	Default model fit on too many SNPs	Filter to sig SNPs (P < 1e-3) before cause(); est_cause_params uses the random subset
MAF column missing -> harmonise action=2 silently downgrades	EAF unavailable	Provide EAF or use action = 3 and document the loss

Tool Installation Notes

# CRAN-stable
install.packages(c('remotes', 'MendelianRandomization', 'MVMR', 'coloc'))

# GitHub-only or recently archived
remotes::install_github('MRCIEU/TwoSampleMR')          # primary orchestrator
remotes::install_github('MRCIEU/ieugwasr')             # OpenGWAS client + local clumping
remotes::install_github('rondolab/MR-PRESSO')          # never on CRAN
remotes::install_github('qingyuanzhao/mr.raps')        # CRAN-archived 2025-03-01
remotes::install_github('jean997/cause')               # depends on mixsqp; suggests Rfast
remotes::install_github('cnfoley/mrclust')             # heterogeneity clusters
remotes::install_github('LizaDarrous/lhcMR')           # bidirectional + heritable confounder
remotes::install_github('HDTian/DRMR')                 # doubly-ranked stratification
remotes::install_github('n-mounier/MRlap')             # joint overlap + winner's-curse + weak-IV correction

TwoSampleMR::mr_raps() is a thin wrapper that calls mr.raps::mr.raps() under the hood; the GitHub mr.raps install above is therefore required. The MendelianRandomization package does NOT export mr_raps() (verify with ls('package:MendelianRandomization')); only TwoSampleMR offers a MR-RAPS entry point. For local clumping, install plink2 and download a 1KG EUR (or matched-ancestry) reference bfile.

STROBE-MR Reporting

STROBE-MR (Skrivankova 2021 JAMA 326:1614; BMJ 375:n2233): 20-item checklist required by Eur J Epi / Nat Genet / JAMA / Diabetologia since 2022. See causal-genomics/pleiotropy-detection for the per-item table -- that skill is the consolidated reporting reference for the full MR + sensitivity battery.

References

• Davey Smith G & Ebrahim S 2003 IJE 32:1 (foundational framework)
• Burgess S & Thompson SG 2017 SAGE textbook (MR canonical reference)
• Bowden J et al 2015 IJE 44:512 (MR-Egger)
• Bowden J et al 2016 Genet Epidemiol 40:304 (weighted median)
• Hartwig FP et al 2017 IJE 46:1985 (weighted mode)
• Zhao Q et al 2020 Ann Stat 48:1742 (MR-RAPS)
• Morrison J et al 2020 Nat Genet 52:740 (CAUSE)
• Zhu Z et al 2018 Nat Commun 9:224 (GSMR + HEIDI)
• Verbanck M et al 2018 Nat Genet 50:693 (MR-PRESSO)
• Sanderson E et al 2019 IJE 48:713 (MVMR conditional F)
• Foley CN et al 2020 Bioinformatics 37:531 (MR-Clust)
• Burgess S et al 2020 Nat Commun 11:376 (contamination mixture)
• O'Connor LJ & Price AL 2018 Nat Genet 50:1728 (LCV)
• Darrous L et al 2021 Nat Commun 12:7274 (LHC-MR)
• Tian H et al 2023 PLoS Genet 19:e1010823 (DRMR)
• Burgess S et al 2016 Genet Epidemiol 40:597 (sample-overlap correction)
• Schmidt AF et al 2020 Nat Commun 11:3255 (drug-target / cis-MR framework)
• Hemani G & Tilling K 2022 Wellcome Open Res 7:14 (Steiger filter caveat)
• Skrivankova VW et al 2021 JAMA 326:1614 (STROBE-MR statement)
• Mounier N & Kutalik Z 2023 Genet Epidemiol 47:314 (MRlap joint correction)
• Sanderson E et al 2021 Stat Med 40:5434 (qhet_mvmr Q-minimization estimator)
• Burgess S & Labrecque JA 2018 Eur J Epidemiol 33:947 (binary outcomes non-collapsibility)
• Hu Y et al 2022 IJE 51:1289 (collider bias in case-only / progression cohorts)
• Bowden J et al 2019 IJE 48:728 (one-sample MR bias formulas)
• Hamilton FW et al 2023 medRxiv 23293658 (NLMR stratum-specific bias critique)
• Sadreev II et al 2024 IJE 52:1209 (winner's curse empirical magnitude)
• Ma S et al 2023 JASA (RIVW rerandomized IVW)

Related Skills

• causal-genomics/colocalization-analysis - Confirm shared causal variant for cis-MR drug-target work
• causal-genomics/pleiotropy-detection - Deep dive on MR-PRESSO, Egger, contamination mixture diagnostics
• causal-genomics/fine-mapping - Credible-set construction at instrument loci before cis-MR
• causal-genomics/mediation-analysis - Two-step MR and MVMR difference method for X -> M -> Y mediation
• causal-genomics/transcriptome-wide-association - TWAS as MR-adjacent framework for gene-level inference
• causal-genomics/proteome-mr-drug-target - Dedicated cis-pQTL drug-target MR workflow with UKB-PPP/deCODE/Fenland and coloc triangulation
• population-genetics/association-testing - GWAS source for instrument selection
• clinical-databases/clinvar-lookup - Annotate instrument SNPs for downstream interpretation