update tests

Zilong-Li · Sep 10, 2024 · 5a5ec56 · 5a5ec56
1 parent fe4b9be
commit 5a5ec56
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Showing 2 changed files with 11 additions and 6 deletions.
diff --git a/R/vcf-compare.R b/R/vcf-compare.R
@@ -48,7 +48,7 @@
 #' test <- system.file("extdata", "imputed.gt.vcf.gz", package="vcfppR")
 #' truth <- system.file("extdata", "imputed.gt.vcf.gz", package="vcfppR")
 #' samples <- "HG00133,HG00143,HG00262"
-#' res <- vcfcomp(test, truth, stats="f1", format=c('GT','GT'), samples=samples)
+#' res <- vcfcomp(test, truth, stats="f1", format=c('GT','GT'), samples=samples, setid=TRUE)
 #' str(res)
 #' @export
 vcfcomp <- function(test, truth,

diff --git a/tests/testthat/test-vcf-comp.R b/tests/testthat/test-vcf-comp.R
@@ -6,7 +6,9 @@ imputedvcf <- system.file("extdata", "imputed.gt.vcf.gz", package="vcfppR")
 test_that("can work for correlation r2 between DS and GT", {
   skip_on_os(c("windows"), arch = NULL)
   samples <- "HG00673,NA10840"
-  res <- vcfcomp(imputedvcf, imputedvcf, bins = c(0,1), by.sample = TRUE, samples = samples, stats = "all")
+  res <- vcfcomp(imputedvcf, imputedvcf, bins = c(0,1),
+                 by.sample = TRUE, samples = samples, stats = "all",
+                 setid = TRUE)
   expect_equal(as.numeric(res$r2[1,]), c(15, 6, 1), tolerance=1e-6)
   expect_identical(unlist(res$f1[[3]]), rep(1,2))
   expect_identical(unlist(res$nrc[[3]]), rep(1,2))
@@ -20,30 +22,33 @@ test_that("can work for r2 with af", {
   names(af) <- d1$id
   affile <- tempfile()
   saveRDS(af, affile)
-  res <- vcfcomp(imputedvcf, rawvcf, stats = "r2", bins = c(0,1), af = affile, samples = samples)
+  res <- vcfcomp(imputedvcf, rawvcf, stats = "r2", bins = c(0,1),
+                 af = affile, samples = samples, setid = TRUE)
   expect_identical(res[[2]][,3], 1)
 })
 
 test_that("can work for F1 score", {
   skip_on_os(c("windows"), arch = NULL)
   samples <- "HG00673,NA10840"
-  res <- vcfcomp(rawvcf, imputedvcf, stats = "f1", samples = samples, by.sample = TRUE, bins = c(0,1))
+  res <- vcfcomp(rawvcf, imputedvcf, stats = "f1", samples = samples,
+                 by.sample = TRUE, bins = c(0,1), setid = TRUE)
   expect_identical(paste0(res$samples, collapse = ","), samples)  
   expect_identical(unlist(res[[2]][[3]]), rep(1,2))
 })
 
 test_that("can work for NRC rate by sample", {
   skip_on_os(c("windows"), arch = NULL)
   samples <- "HG00673,NA10840"
-  res <- vcfcomp(rawvcf, imputedvcf, stats = "nrc", samples = samples, by.sample = TRUE, bins = c(0,1))
+  res <- vcfcomp(rawvcf, imputedvcf, stats = "nrc", samples = samples,
+                 by.sample = TRUE, bins = c(0,1), setid = TRUE)
   expect_identical(paste0(res$samples, collapse = ","), samples)  
   expect_identical(unlist(res[[2]][[3]]), rep(1,2))
 })
 
 test_that("can work for PSE", {
   skip_on_os(c("windows"), arch = NULL)
   samples <- "HG00151,HG00380"
-  (res <- vcfcomp(imputedvcf, imputedvcf, stats = "pse", samples = samples))
+  (res <- vcfcomp(imputedvcf, imputedvcf, stats = "pse", samples = samples, setid = TRUE))
   expect_true(is.nan(res[[2]][[1]]$pse))
   expect_true((res[[2]][[2]]$pse==0))
   expect_true((res[[2]][[2]]$disc==0))