properly errors

privefl · Nov 25, 2024 · 184094c · 184094c
1 parent b57ef5b
commit 184094c
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Showing 7 changed files with 24 additions and 6 deletions.
diff --git a/DESCRIPTION b/DESCRIPTION
@@ -2,8 +2,8 @@ Encoding: UTF-8
 Package: bigsnpr
 Type: Package
 Title: Analysis of Massive SNP Arrays
-Version: 1.12.16
-Date: 2024-09-24
+Version: 1.12.17
+Date: 2024-11-25
 Authors@R: c(
     person("Florian", "Privé", email = "[email protected]", role = c("aut", "cre")),
     person("Michael", "Blum", role = "ths"),

diff --git a/NEWS.md b/NEWS.md
@@ -1,3 +1,7 @@
+## bigsnpr 1.12.17
+
+- Now properly errors when `ncol(G) != length(infos.chr)` in `snp_clumping()`. Also when `nrow(gwas) != length(infos.chr)` in `snp_manhattan()`.
+
 ## bigsnpr 1.12.16
 
 - Add function `snp_projectSelfPCA()` (only `bed_projectSelfPCA()` existed).

diff --git a/R/clumping.R b/R/clumping.R
@@ -70,11 +70,13 @@ snp_clumping <- function(G, infos.chr,
                          ncores = 1) {
 
   check_args()
+  assert_lengths(infos.chr, cols_along(G))
 
   if (!missing(is.size.in.bp))
     warning2("Parameter 'is.size.in.bp' is deprecated.")
 
-  if (!is.null(S)) assert_lengths(infos.chr, S)
+  if (!is.null(infos.pos)) assert_lengths(infos.pos, infos.chr)
+  if (!is.null(S)) assert_lengths(S, infos.chr)
 
   ind.noexcl <- setdiff(seq_along(infos.chr), exclude)
 

diff --git a/R/man-qq-gc.R b/R/man-qq-gc.R
@@ -45,6 +45,7 @@ snp_manhattan <- function(gwas, infos.chr, infos.pos,
                           coeff = 1) {
 
   check_args(infos.chr = "")
+  assert_lengths(infos.chr, infos.pos, rows_along(gwas))
 
   # get ordering
   ord <- order(infos.chr, infos.pos)

diff --git a/docs/news/index.html b/docs/news/index.html
diff --git a/tests/testthat/test-2-bed-clumping-SVD.R b/tests/testthat/test-2-bed-clumping-SVD.R
@@ -21,6 +21,10 @@ test_that("Scales work", {
 
 POS <- bigSNP$map$physical.pos
 CHR0 <- sort(rep_len(1:2, ncol(G)))
+expect_error(snp_clumping(G, infos.chr = CHR0[1:5], infos.pos = POS),
+             "Incompatibility between dimensions")
+expect_error(snp_clumping(G, infos.chr = CHR0, infos.pos = POS[1:5]),
+             "Incompatibility between dimensions")
 ind.keep0 <- snp_clumping(G, infos.chr = CHR0, infos.pos = POS,
                           exclude = which(CHR0 == 1))
 expect_true(all(CHR0[ind.keep0] == 2))

diff --git a/tests/testthat/test-4-manhattan.R b/tests/testthat/test-4-manhattan.R
@@ -9,6 +9,9 @@ test_that("snp_manhattan() works with unordered data", {
   N <- ncol(G)
   CHR <- sort(rep_len(1:2, N))
   POS <- 1:N * 1000
+  expect_error(snp_manhattan(gwas, CHR[1:5], POS[1:5]),
+               "Incompatibility between dimensions")
+
   rand <- sample(N)
   # plot_grid(
   #   snp_manhattan(gwas, CHR, POS, dist.sep.chrs = 0),