inst/unitTests/test_NanoStringRccSet-accessors.R

In Nanostring-Biostats/NanoStringNCTools: NanoString nCounter Tools

rcc <-
  NanoStringRccSet(assayData =
         matrix(0:11, 4L, 3L,
                dimnames = list(letters[1:4], sprintf("%s.RCC", LETTERS[1:3]))),
       phenoData =
         AnnotatedDataFrame(data.frame(Treatment = c("A", "A", "B"),
                                       Age = c(58L, 42L, 27L),
                                       row.names = sprintf("%s.RCC", LETTERS[1:3]),
                                       stringsAsFactors = FALSE),
                            dimLabels = c("sampleNames", "sampleColumns")),
       featureData =
         AnnotatedDataFrame(data.frame(CodeClass = c("Endogenous", "Positive", "Negative", "Housekeeping"),
                                       GeneName = letters[1:4],
                                       Accession = letters[1:4],
                                       IsControl = c(FALSE, TRUE, TRUE, TRUE),
                                       ControlConc = c(NA_real_, 0.125, 0, NA_real_),
                                       row.names = letters[1:4],
                                       stringsAsFactors = FALSE),
                            dimLabels = c("featureNames", "featureColumns")),
       annotation = "rlffile",
       protocolData =
         AnnotatedDataFrame(data.frame(FileVersion = numeric_version(rep("1.7", 3L)),
                                       SoftwareVersion = numeric_version(rep("4.0.0.3", 3L)),
                                       SystemType = rep("Gen2", 3L),
                                       SampleID = letters[1:3],
                                       SampleOwner = rep("", 3L),
                                       SampleComments = rep("DNA-RNA-Protein", 3L),
                                       SampleDate = as.Date(rep("1999-12-31", 3L)),
                                       SystemAPF = rep("n6_vDV1", 3L),
                                       AssayType = rep(NA_character_, 3L),
                                       LaneID = 1:3,
                                       FovCount = rep(280L, 3L),
                                       FovCounted = 1:3,
                                       ScannerID = rep("a", 3L),
                                       StagePosition = 1:3,
                                       BindingDensity = c(0.75, 1, 1.25),
                                       CartridgeID = letters[1:3],
                                       CartridgeBarcode = rep("", 3L),
                                       row.names = sprintf("%s.RCC", LETTERS[1:3]),
                                       stringsAsFactors = FALSE),
                            NanoStringNCTools:::.rccMetadata[["protocolData"]],
                            dimLabels = c("sampleNames", "sampleColumns"))
  )


# Accessing
test_NanoStringRccSet_sData <- function() {
  checkIdentical(cbind(pData(rcc), pData(protocolData(rcc))), sData(rcc))
}

test_NanoStringRccSet_svarLabels <- function() {
  checkIdentical(c(varLabels(rcc), varLabels(protocolData(rcc))), svarLabels(rcc))
}