TwoSampleMR 0.7.1

DESCRIPTION

@@ -1,7 +1,7 @@
 Package: TwoSampleMR
 Title: Two Sample MR Functions and Interface to MRC Integrative
     Epidemiology Unit OpenGWAS Database
-Version: 0.7.0
+Version: 0.7.1
 Authors@R: c(
     person("Gibran", "Hemani", , "g.hemani@bristol.ac.uk", role = c("aut", "cre"),
            comment = c(ORCID = "0000-0003-0920-1055")),

NEWS.md

@@ -1,3 +1,10 @@
+# TwoSampleMR v0.7.1
+
+(Release date 2026-03-25)
+
+* Added error message if unsupported method listed in the `method_list` argument to the `mr()` function (thanks @42kuroniko)
+* Added warning if `mr_wald_ratio()` passed more than one genotype's summary statistics
+
 # TwoSampleMR v0.7.0
 
 (Release date 2026-02-24)

R/mr.R

@@ -15,6 +15,25 @@ mr <- function(
   parameters = default_parameters(),
   method_list = subset(mr_method_list(), use_by_default)$obj
 ) {
+  supported_methods <- mr_method_list()$obj
+  unsupported <- setdiff(method_list, supported_methods)
+  if (length(unsupported) > 0) {
+    msg <- paste0(
+      "The following methods are not supported by mr(): ",
+      paste(unsupported, collapse = ", "),
+      ".\nSupported methods are: ",
+      paste(supported_methods, collapse = ", "),
+      "."
+    )
+    if (any(unsupported %in% c("mr_presso", "run_mr_presso"))) {
+      msg <- paste0(
+        msg,
+        "\nFor MR-PRESSO, please use run_mr_presso() instead of mr()."
+      )
+    }
+    stop(msg)
+  }
+
   if ("mr_raps" %in% method_list) {
     if (!(requireNamespace("mr.raps", quietly = TRUE))) {
       stop(
@@ -311,6 +330,14 @@ default_parameters <- function() {
 #' }
 mr_wald_ratio <- function(b_exp, b_out, se_exp, se_out, parameters) {
   if (length(b_exp) > 1) {
+    warning(
+      "mr_wald_ratio requires exactly one SNP, but ",
+      length(b_exp),
+      " were provided. ",
+      "Use a method that supports multiple SNPs (e.g. mr_ivw) or subset your data to a single SNP. ",
+      "Returning NA.",
+      call. = FALSE
+    )
     return(list(b = NA, se = NA, pval = NA, nsnp = NA))
   }
   b <- b_out / b_exp

tests/testthat/test_eve.R

@@ -5,7 +5,7 @@ load(system.file("extdata", "test_commondata.RData", package = "TwoSampleMR"))
 
 test_that("wrapper", {
   skip_if_not_installed("car")
-  expect_warning(w <- mr_wrapper(dat))
+  w <- expect_warning(mr_wrapper(dat))
   expect_true(length(w) == 1)
   expect_true(length(names(w[[1]])) == 5)
 })

tests/testthat/test_mr.R

@@ -69,3 +69,24 @@ test_that("mr_grip() not from mr()", {
   expect_equal(tst$se.adj, 0.16389, tol = 1e-4)
   expect_equal(tst$nsnp, 79L)
 })
+
+test_that("Including MR-PRESSO in the list", {
+  expect_error(res7 <- mr(dat, method_list = c("mr_presso")))
+})
+
+test_that("Including MR-PRESSO in the list", {
+  expect_error(res8 <- mr(dat, method_list = c("run_mr_presso")))
+})
+
+test_that("mr_wald_ratio works with a single SNP", {
+  res9 <- mr(dat[1, ], method_list = "mr_wald_ratio")
+  expect_equal(nrow(res9), 1L)
+})
+
+test_that("mr_wald_ratio warns with multiple SNPs and returns 0 rows", {
+  res10 <- expect_warning(
+    mr(dat, method_list = "mr_wald_ratio"),
+    "mr_wald_ratio requires exactly one SNP"
+  )
+  expect_equal(nrow(res10), 0L)
+})

tests/testthat/test_otherformats.R

@@ -30,7 +30,7 @@ test_that("MRInput with cor", {
 
 
 test_that("mrpresso", {
-  expect_warning(w <- run_mr_presso(dat))
+  w <- expect_warning(run_mr_presso(dat))
   expect_true(length(w) == 1)
   expect_true(class(w) == "list")
   expect_true(class(w[[1]]) == "list")

tests/testthat/test_plots.R

@@ -55,8 +55,8 @@ rm(list = ls())
 load(system.file("extdata", "forestplot_1_to_many_data.RData", package = "TwoSampleMR"))
 
 test_that("Forest plot 1 to many", {
-  expect_warning(
-    p8 <- forest_plot_1_to_many(
+  p8 <- expect_warning(
+    forest_plot_1_to_many(
       res,
       b = "b",
       se = "se",
@@ -113,8 +113,8 @@ test_that("Forest plot 1 to many test 3 - with subcategory in by argument", {
   res$subcategory[is.na(res$subcategory)] <- "Group 2"
   res$weight <- 1 / res$se
   res <- sort_1_to_many(res, sort_action = 1, group = "subcategory")
-  expect_warning(
-    p10 <- forest_plot_1_to_many(
+  p10 <- expect_warning(
+    forest_plot_1_to_many(
       res,
       b = "b",
       se = "se",

tests/testthat/test_steiger.R

@@ -21,6 +21,6 @@ test_that("directionality cc", {
 })
 
 test_that("steiger filtering", {
-  expect_warning(dat <- steiger_filtering(dat))
+  dat <- expect_warning(steiger_filtering(dat))
   expect_true("steiger_pval" %in% names(dat))
 })