tests/testthat/test_checkGeneSymbols.R

In HGNChelper: Identify and Correct Invalid HGNC Human Gene Symbols and MGI Mouse Gene Symbols

## human test 1
x = c("FN1", "TP53", "UNKNOWNGENE","7-Sep", "9/7", "1-Mar", "Oct4", "4-Oct",
      "OCT4-PG4", "C19ORF71", "C19orf71")

expect_warning(res <- checkGeneSymbols(x))

expect_equal(sum(res[,1] != x), 0)
expect_equal(res[,2],
  c(TRUE,TRUE,FALSE,FALSE,FALSE,FALSE,FALSE,FALSE,FALSE,FALSE,TRUE))

expected.correct <- c("FN1","TP53",NA,"SEPTIN7","SEPTIN7","MTARC1 /// MARCHF1",
                      "POU5F1","POU5F1","POU5F1P4","C19orf71","C19orf71")

expect_equal(as.character(res[,3]), expected.correct)

expect_warning(res2 <- checkGeneSymbols(x, unmapped.as.na = FALSE))
expect_identical(res[, 1:2], res2[, 1:2])
unmapped <- is.na(res[, 3])
expect_identical(res2[unmapped, 3], res2[unmapped, 1])

## human test 2
x = c("C21orf62-AS1", "c21orf62-as1",
      "MORF4L1P7", "Morf4L1P7",
      "Fn1", "FN1",
      "TP53",
      "UNKNOWNGENE",
      "7-Sep", "1-Mar", "1-MAR")

expect_warning(res <- checkGeneSymbols(x))
answers <- c(TRUE, FALSE,
             TRUE, FALSE,
             FALSE, TRUE,
             TRUE,
             FALSE,
             FALSE, FALSE, FALSE)
expect_equal(sum(res[,1] != x), 0)
expect_equal(sum(res[,2] != answers), 0)
expect_equal(as.character(res[,3]), c("C21orf62-AS1", "C21orf62-AS1",
                                              "MORF4L1P7", "MORF4L1P7",
                                              "FN1", "FN1",
                                              "TP53",
                                              NA,
                                              "SEPTIN7", "MTARC1 /// MARCHF1", "MTARC1 /// MARCHF1"))

# mouse test 1
data(mouse.table)
orig <- c("1-Feb", "A2m", "A2mr", "UNKNOWNGENE")
correct <- c("Feb1", "AI893533", "A2mr", NA)
expect_warning(res <- checkGeneSymbols(orig, species="mouse"))
expect_equal(res$Approved, c(FALSE, FALSE, TRUE, FALSE))
expect_equal(res$Suggested.Symbol, correct)

# check capitalization behavior
orig <- c("tp53", "TP53")
data("hgnc.table", package="HGNChelper", envir = environment())
expect_warning(res <- checkGeneSymbols(orig, species=NULL, map=hgnc.table))
expect_equal(res$Suggested.Symbol, c(NA, "TP53"))
expect_warning(res <- checkGeneSymbols(orig, species="human", map=hgnc.table))
expect_equal(res$Suggested.Symbol, c("TP53", "TP53"))
expect_warning(res <- checkGeneSymbols(orig, map=hgnc.table))
expect_equal(res$Suggested.Symbol, c("TP53", "TP53"))

# check specifying manual map
mymap <- data.frame(Symbol=c("A", "B", "BB"), Approved.Symbol=c("A", "BB", "BB"), stringsAsFactors = FALSE)
# with no human capitalization help
expect_warning(res <- checkGeneSymbols(c("a", "b", "A", "B", "BB"), map=mymap, species=NULL))
expect_equal(res$Approved, c(FALSE, FALSE, TRUE, FALSE, TRUE))
expect_equal(res$Suggested.Symbol, c(NA, NA, "A", "BB", "BB"))
# with human capitalization help
expect_warning(res <- checkGeneSymbols(c("a", "b", "A", "B", "BB"), map=mymap, species="human"))
expect_equal(res$Approved, c(FALSE, FALSE, TRUE, FALSE, TRUE))
expect_equal(res$Suggested.Symbol, c("A", "BB", "A", "BB", "BB"))

expect_error(checkGeneSymbols(c("a", "b", "A", "B", "BB"), map=as.matrix(mymap)))
expect_error(checkGeneSymbols(c("a", "b", "A", "B", "BB"), map=NULL, species=NULL))
expect_warning(res2 <- checkGeneSymbols(factor(c("a", "b", "A", "B", "BB")), map=mymap, species="human"))
expect_identical(res, res2)

# check for outdated symbols from extdata/mog_map.csv
expect_warning(res3 <-
                 checkGeneSymbols(c("MARC1", "MARC2", "MARCH6")))
expect_equal(res3$Approved, rep(FALSE, 3))
expect_equal(res3$Suggested.Symbol, c("MTARC1", "MTARC2", "MARCHF6"))