Adjust tests and examples for change in capitalization

waldronlab · Dec 21, 2023 · 3f6ee5c · 3f6ee5c
1 parent b2c3d1a
commit 3f6ee5c
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Showing 4 changed files with 6 additions and 5 deletions.
diff --git a/R/getSignatures.R b/R/getSignatures.R
@@ -98,7 +98,7 @@ getSignatures <- function(df,
 #'
 #'  # Condition-specific meta-signatures from fecal samples, increased
 #'  # in conditions of study. Use taxonomic names instead of the default NCBI IDs:
-#'  df.feces <- df[df$`Body site` == "feces", ]
+#'  df.feces <- df[tolower(df$`Body site`) == "feces", ]
 #'  cond.meta.sigs <- getMetaSignatures(df.feces, column = "Condition", 
 #'                                      direction = "UP", tax.id.type = "taxname")
 #'

diff --git a/man/getMetaSignatures.Rd b/man/getMetaSignatures.Rd
diff --git a/tests/testthat/test-getMetaSignatures.R b/tests/testthat/test-getMetaSignatures.R
@@ -1,5 +1,5 @@
 bsdb <- importBugSigDB()
-df.feces <- subset(bsdb, `Body site` == "feces")
+df.feces <- subset(bsdb, `Body site` == "Feces")
 bs.msigs <- getMetaSignatures(bsdb, "Body site")
 co.msigs <- getMetaSignatures(df.feces, "Condition")
 

diff --git a/tests/testthat/test-ontology.R b/tests/testthat/test-ontology.R
@@ -20,12 +20,13 @@ checkOnto <- function(onto, which = c("efo", "uberon"))
 
 checkSubset <- function(sdf, col, pos, neg)
 {
+    print(paste(pos,"and",neg))
     expect_true(is.data.frame(sdf))
     expect_true(nrow(sdf) > 0)
     rel.cols <- c("Body site", "Condition")
     expect_true(all(rel.cols %in% colnames(sdf)))
-    expect_true(all(pos %in% sdf[,col]))
-    expect_false(any(neg %in% sdf[,col]))
+    expect_true(all(tolower(pos) %in% tolower(sdf[,col])))
+    expect_false(any(tolower(neg) %in% tolower(sdf[,col])))
 } 
 
 test_that("getOntology", {