Fixed the removal of duplicated proxy SNPs in extract_outcome_data()

DESCRIPTION

@@ -1,7 +1,7 @@
 Package: TwoSampleMR
 Title: Two Sample MR Functions and Interface to MRC Integrative
     Epidemiology Unit OpenGWAS Database
-Version: 0.7.9
+Version: 0.7.10
 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 +1,9 @@
+# TwoSampleMR v0.7.10
+
+(Release date 2026-09-24)
+
+* Fixed the removal of duplicated proxy SNPs in `extract_outcome_data()`, which since v0.6.30 ignored its intended grouping by outcome and emitted the warning "Ignoring by/keyby because 'j' is not supplied" whenever proxies were used. Results were unaffected because proxies are looked up one outcome at a time. (thanks @amymariemason for the report)
+
 # TwoSampleMR v0.7.9
 
 (Release date 2026-06-24)

R/query.R

@@ -286,7 +286,7 @@ format_d <- function(d) {
 
     # If two SNPs have the same proxy SNP then one has to be removed
     d <- data.table::as.data.table(d)
-    d <- d[!duplicated(proxy_snp.outcome), , by = outcome]
+    d <- d[!duplicated(d, by = c("outcome", "proxy_snp.outcome"))]
     data.table::setDF(d)
   } else {
     d <- d1

justfile

@@ -1,8 +1,16 @@
 docs:
-    R -e "devtools::document()"
+    Rscript -e "devtools::document()"
 check: docs
-    R -e "devtools::check()"
+    Rscript -e "devtools::check()"
+test:
+    Rscript -e "devtools::test()"
+test-server:
+    TWOSAMPLEMR_ENABLE_OPENGWAS_TESTS=TRUE Rscript -e "devtools::test()"
 install: docs
-    R -e "devtools::install(build_vignettes = TRUE)"
+    Rscript -e "devtools::install(build_vignettes = TRUE)"
+install-fast: docs
+    Rscript -e "pkg <- pkgbuild::build(dest_path = tempdir(), vignettes = FALSE); install.packages(pkg, repos = NULL, type = 'source')"
 dev:
-    R -e "pak::local_install_dev_deps()"
+    Rscript -e "pak::local_install_dev_deps()"
+readme:
+    Rscript -e "rmarkdown::render('README.Rmd', output_options = list(html_preview = FALSE))"

tests/testthat/test_format_d.R

@@ -0,0 +1,26 @@
+test_that("format_d() removes duplicated proxy SNPs within each outcome without warning", {
+  d <- data.frame(
+    rsid = c("rs1", "rs2", "rs1", "rs2"),
+    chr = "1",
+    position = c(100, 200, 100, 200),
+    beta = 0.1,
+    se = 0.01,
+    n = 1000,
+    p = 1e-8,
+    eaf = 0.3,
+    ea = "A",
+    nea = "G",
+    trait = c("Trait A", "Trait A", "Trait B", "Trait B"),
+    id = c("id-a", "id-a", "id-b", "id-b"),
+    proxy = TRUE,
+    target_snp = c("rs1", "rs2", "rs1", "rs2"),
+    proxy_snp = "rs3",
+    target_a1 = "A",
+    target_a2 = "G",
+    proxy_a1 = "A",
+    proxy_a2 = "G"
+  )
+  expect_no_warning(out <- format_d(d))
+  expect_equal(nrow(out), 2)
+  expect_setequal(out$id.outcome, c("id-a", "id-b"))
+})