Merge pull request #664 from remlapmot/v0-6-27

Remove an unused argument from `extract_instruments()` and `clump_data()`

Author: remlapmot

.Rbuildignore

@@ -20,3 +20,4 @@ cache$
 ^\.lintr$
 ^inst/sandpit$
 ^air\.toml$
+^vignettes/rf\.rdata$

.github/workflows/pkgdown.yaml

@@ -21,6 +21,7 @@ jobs:
       group: pkgdown-${{ github.event_name != 'pull_request' || github.run_id }}
     env:
       GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }}
+      OPENGWAS_X_TEST_MODE_KEY: ${{ secrets.OPENGWAS_X_TEST_MODE_KEY }}
     permissions:
       contents: write
     steps:

.gitignore

@@ -25,3 +25,4 @@ vignettes/plot1.pdf
 vignettes/mr_report.md
 vignettes/figure/*.png
 vignettes/*.html
+rf.rdata

DESCRIPTION

@@ -1,7 +1,7 @@
 Package: TwoSampleMR
 Title: Two Sample MR Functions and Interface to MRC Integrative
     Epidemiology Unit OpenGWAS Database
-Version: 0.6.26
+Version: 0.6.27
 Authors@R: c(
     person("Gibran", "Hemani", , "[email protected]", role = c("aut", "cre"),
            comment = c(ORCID = "0000-0003-0920-1055")),

NEWS.md

@@ -1,3 +1,9 @@
+# TwoSampleMR v0.6.27
+
+(Release date 2025-12-15)
+
+* Removed the unused `p2` argument from `extract_instruments()` and the unused `clump_p2` argument from `clump_data()` (thanks @yikeshu0611).
+
 # TwoSampleMR v0.6.26
 
 (Release date 2025-12-12)

R/instruments.R

@@ -6,7 +6,6 @@
 #' @param outcomes Array of outcome IDs (see [available_outcomes()]).
 #' @param p1 Significance threshold. The default is `5e-8`.
 #' @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.
@@ -18,7 +17,6 @@ extract_instruments <- function(
   outcomes,
   p1 = 5e-8,
   clump = 1,
-  p2 = 5e-8,
   r2 = 0.001,
   kb = 10000,
   opengwas_jwt = ieugwasr::get_opengwas_jwt(),

R/ld.R

@@ -16,7 +16,6 @@
 #' @param clump_kb Clumping window, default is `10000`.
 #' @param clump_r2 Clumping r2 cutoff. Note that this default value has recently changed from `0.01` to `0.001`.
 #' @param clump_p1 Clumping sig level for index SNPs, default is `1`.
-#' @param clump_p2 Clumping sig level for secondary SNPs, default is `1`.
 #' @param pop Super-population to use as reference panel. Default = `"EUR"`. Options are `"EUR"`, `"SAS"`, `"EAS"`, `"AFR"`, `"AMR"`. `'legacy'` also available - which is a previously used version of the EUR panel with a slightly different set of markers
 #' @param bfile If this is provided then will use the API. Default = `NULL`
 #' @param plink_bin If `NULL` and `bfile` is not `NULL` then will detect packaged plink binary for specific OS. Otherwise specify path to plink binary. Default = `NULL`
@@ -28,7 +27,6 @@ clump_data <- function(
   clump_kb = 10000,
   clump_r2 = 0.001,
   clump_p1 = 1,
-  clump_p2 = 1,
   pop = "EUR",
   bfile = NULL,
   plink_bin = NULL