Merge pull request #663 from remlapmot/fix-extract-instruments-arg

Fix two issues in `extract_instruments()`

Author: remlapmot

DESCRIPTION

@@ -1,7 +1,7 @@
 Package: TwoSampleMR
 Title: Two Sample MR Functions and Interface to MRC Integrative
     Epidemiology Unit OpenGWAS Database
-Version: 0.6.25
+Version: 0.6.26
 Authors@R: c(
     person("Gibran", "Hemani", , "[email protected]", role = c("aut", "cre"),
            comment = c(ORCID = "0000-0003-0920-1055")),

NEWS.md

@@ -1,3 +1,10 @@
+# TwoSampleMR v0.6.26
+
+(Release date 2025-12-12)
+
+* Fixed the passing of the `force_server` argument within `extract_instruments()` through to `ieugwasr::tophits()` (thanks @yikeshu0611).
+* Amended the `extract_instruments()` `clump` argument to additionally take values `1` or `0` as per the `ieugwasr::tophits()` `clump` argument (thanks @yikeshu0611).
+
 # TwoSampleMR v0.6.25
 
 (Release date 2025-12-05)

R/instruments.R

@@ -5,25 +5,28 @@
 #'
 #' @param outcomes Array of outcome IDs (see [available_outcomes()]).
 #' @param p1 Significance threshold. The default is `5e-8`.
-#' @param clump Logical; whether to clump results. The default is `TRUE`.
+#' @param clump Whether to clump results (`1`) or not (`0`). Default is `1`. (`TRUE` and `FALSE` are also allowed for backwards compatibility.)
 #' @param p2 Secondary clumping threshold. The default is `5e-8`.
 #' @param r2 Clumping r2 cut off. The default is `0.001`.
 #' @param kb Clumping distance cutoff. The default is `10000`.
 #' @param opengwas_jwt Used to authenticate protected endpoints. Login to <https://api.opengwas.io> to obtain a jwt. Provide the jwt string here, or store in .Renviron under the keyname OPENGWAS_JWT.
-#' @param force_server Force the analysis to extract results from the server rather than the MRInstruments package.
+#' @param force_server Whether to search through pre-clumped dataset or to re-extract and clump directly from the server. The default is `FALSE`.
 #'
 #' @export
 #' @return data frame
 extract_instruments <- function(
   outcomes,
   p1 = 5e-8,
-  clump = TRUE,
+  clump = 1,
   p2 = 5e-8,
   r2 = 0.001,
   kb = 10000,
   opengwas_jwt = ieugwasr::get_opengwas_jwt(),
   force_server = FALSE
 ) {
+  if (!(clump %in% c(0, 1, FALSE, TRUE))) stop("The clump argument should be 0 or 1.")
+  if (clump) clump <- 1
+  if (!clump) clump <- 0
   # .Deprecated("ieugwasr::tophits()")
   outcomes <- ieugwasr::legacy_ids(unique(outcomes))
 
@@ -33,7 +36,7 @@ extract_instruments <- function(
     clump = clump,
     r2 = r2,
     kb = kb,
-    force_server = FALSE,
+    force_server = force_server,
     opengwas_jwt = opengwas_jwt,
     x_api_source = x_api_source_header()
   )

man/extract_instruments.Rd

@@ -6,7 +6,7 @@ skip_if_offline(host = "api.opengwas.io")
 skip_on_cran()
 
 # extract some data
-a <- try(extract_instruments("ieu-a-2", clump = FALSE))
+a <- try(extract_instruments("ieu-a-2", clump = 0))
 if (class(a) == "try-error") {
   skip("Server issues")
 }
@@ -37,7 +37,7 @@ test_that("matrix", {
 
 
 test_that("clump multiple", {
-  a <- try(extract_instruments(c("ieu-a-2", "ieu-a-1001"), clump = FALSE))
+  a <- try(extract_instruments(c("ieu-a-2", "ieu-a-1001"), clump = 0))
   if (class(a) == "try-error") {
     skip("Server issues")
   }