inst/unitTests/test_GeneHancerDB.R

In PriceLab/TrenaProjectHG38: TrenaProjectHG38 - an abstract base class for all hg38 projects

# test_GeneHancerDB.R
#------------------------------------------------------------------------------------------------------------------------
library(TrenaProjectHG38)
library(RUnit)
#------------------------------------------------------------------------------------------------------------------------
if(!exists("ghdb")){
   ghdb <- GeneHancerDB()
   } # creating for several tests below

#------------------------------------------------------------------------------------------------------------------------
runTests <- function()
{
   test_ctor()
   test_listTissues()
   test_.eliminateDupsCollapseTissues()
   test_foxo6()
   test_failureByTissue()
   test_queryUnknownGene()

} # runTests
#------------------------------------------------------------------------------------------------------------------------
test_ctor <- function()
{
   message(sprintf("--- test_ctor"))
   checkTrue("GeneHancerDB" %in% is(ghdb))

} # test_ctor
#------------------------------------------------------------------------------------------------------------------------
test_listTissues <- function()
{
   message(sprintf("--- test_listTissues"))
   tissues <- listTissues(ghdb)
   checkTrue(length(tissues) > 300)
   checkTrue(all(c("placenta", "Placenta") %in% tissues))

   tissues.gata2 <- listTissues(ghdb, targetGene="GATA2")
   checkTrue(length(tissues.gata2) > 120)
   checkTrue(length(tissues.gata2) < 130)

} # test_listTissues
#------------------------------------------------------------------------------------------------------------------------
test_.eliminateDupsCollapseTissues <- function()
{
   message(sprintf("--- test_.eliminateDupsCollapseTissues"))

   load(system.file(package="TrenaProjectHG38", "extdata", "testing", "tbl.gh.results.toTestReductionPreservingTissues.RData"))
   checkEquals(dim(tbl), c(956, 17))
   tbl.trimmed <- TrenaProjectHG38:::.eliminateDupsCollapseTissues(tbl)
   checkEquals(dim(tbl.trimmed), c(50, 16))

      # do a rough assay of the collapsed tissue column
   spread <- fivenum(nchar(tbl.trimmed$tissue))  # [1]   16   62  156  338 2213
   checkTrue(spread[1] < 20)
   checkTrue(spread[5] > 2000)

} # test_.eliminateDupsCollapseTissues
#------------------------------------------------------------------------------------------------------------------------
# a simple test case, chosen for historical (and no longer important) reasons
test_foxo6 <- function()
{
   message(sprintf("--- test_foxo6"))

      # ENCODE and Ensembl use different capitalization
   tissues <-  c("placenta", "Placenta")
   tbl <- retrieveEnhancersFromDatabase(ghdb, "FOXO6", tissues)
   checkTrue(is.data.frame(tbl))
   checkEquals(nrow(tbl), 13)
   checkTrue(all(tissues %in% tbl$tissue))
   checkEquals(length(which(duplicated(tbl$sig))), 0)  # no duplicated regions
   checkTrue(length(grep(";", tbl$tissue)) > 0)        # 4 instances of "Placenta;placenta"

   tbl.all <- retrieveEnhancersFromDatabase(ghdb, "FOXO6", tissues="all")
   checkTrue(is.data.frame(tbl.all))
   checkEquals(nrow(tbl.all), 43)
   checkEquals(length(which(duplicated(tbl.all$sig))), 0)  # no duplicated regions
   checkTrue(max(nchar(tbl.all$tissue)) > 2000)
   checkTrue(length(grep(";", tbl.all$tissue)) > 40)       # most tissue values are semicolor separated multiples

} # test_gata6
#------------------------------------------------------------------------------------------------------------------------
# a simple test case, chosen for historical (and no longer important) reasons
test_failureByTissue <- function()
{
   message(sprintf("--- test_failureByTissue"))

   trem2.tissues <- retrieveEnhancersFromDatabase(ghdb, "TREM2", tissues="all")$tissue
   tissues <-  c("brain", "Brain")
   checkTrue(length(intersect(tissues, trem2.tissues)) == 0)

   suppressWarnings(
      tbl <- retrieveEnhancersFromDatabase(ghdb, "TREM2", tissues)
      )
   checkEquals(nrow(tbl), 0)

      # double check now that at least one tissue reports for TREM2
   tbl <- retrieveEnhancersFromDatabase(ghdb, "TREM2", "placenta")
   checkTrue(nrow(tbl) > 0)

} # test_failureByTissue
#------------------------------------------------------------------------------------------------------------------------
test_queryUnknownGene <- function()
{
   message(sprintf("--- test_queryUnknownGene"))
   symbol <- "LINC00982"
   tbl <- retrieveEnhancersFromDatabase(ghdb, symbol, tissues="all")


} # test_queryUnknownGene
#------------------------------------------------------------------------------------------------------------------------
if(!interactive())
   runTests()