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M1 <- matrix(1, 5, 3)
M2 <- matrix(1, 3, 3)
assaysList <- list(gr=SimpleList(m=M1), grl=SimpleList(m=M2))
rowRangesList <-
list(gr=GRanges("chr1", IRanges(1:5, 10)),
grl=split(GRanges("chr1", IRanges(1:5, 10)), c(1,1,2,2,3)))
names(rowRangesList[["grl"]]) <- NULL
colData <- DataFrame(x=letters[1:3])
## a list of one SE with GRanges and one with GRangesList
rseList <-
list(SummarizedExperiment(
assays=assaysList[["gr"]],
rowRanges=rowRangesList[["gr"]],
colData=colData),
SummarizedExperiment(
assays=assaysList[["grl"]],
rowRanges=rowRangesList[["grl"]],
colData=colData))
test_SummarizedExperiment_GenomicRanges_coercion <- function()
{
eset1 <- ExpressionSet()
checkTrue(validObject(eset1))
se1 <- as(eset1, "RangedSummarizedExperiment")
checkTrue(validObject(se1))
data("sample.ExpressionSet", package = "Biobase")
eset2 <- sample.ExpressionSet
checkTrue(validObject(eset2))
se2 <- as(eset2, "RangedSummarizedExperiment")
checkTrue(validObject(se2))
checkIdentical(experimentData(eset2),
metadata(se2)$experimentData)
checkIdentical(annotation(eset2),
metadata(se2)$annotation)
checkIdentical(protocolData(eset2),
metadata(se2)$protocolData)
eset2Assays <- SimpleList(as.list(assayData(eset2)))
se2Assays <- assays(se2)
checkIdentical(eset2Assays$exprs, se2Assays$exprs)
checkIdentical(eset2Assays$se.exprs, se2Assays$se.exprs)
checkIdentical(featureNames(eset2), rownames(se2))
checkIdentical(sampleNames(eset2), colnames(se2))
}
test_GenomicRanges_SummarizedExperiment_coercion <- function()
{
## empty SE
simpleSE <- SummarizedExperiment()
eset1 <- as(simpleSE, "ExpressionSet")
checkTrue(validObject(eset1))
## Back and forth empty ES
simpleES <- ExpressionSet()
simpleES2 <- as(as(simpleES, "RangedSummarizedExperiment"),
"ExpressionSet")
checkTrue(validObject(simpleES2))
checkEquals(as.list(assayData(simpleES)),
as.list(assayData(simpleES2)))
## Simple SE
simpleSE <- rseList[[1]]
assayNames(simpleSE) <- "exprs" # No warning 'No assay named exprs..."
eset2 <- as(simpleSE, "ExpressionSet")
checkTrue(validObject(eset2))
## The ExpressionSet features should have the data from the
## SummarizedExperiment rows if they are from GRanges.
checkIdentical(pData(featureData(eset2)),
as.data.frame(rowRanges(rseList[[1]])))
# the rowRanges are retained if the object has them to begin with.
se2_2 <- as(eset2, "RangedSummarizedExperiment")
rr_se2_2 <- unname(rowRanges(se2_2))
rr_eset2 <- rowRanges(rseList[[1]])
checkEquals(rr_se2_2, rr_eset2)
simpleSE <- rseList[[2]]
assayNames(simpleSE) <- "exprs" # No warning 'No assay named exprs..."
eset3 <- as(simpleSE, "ExpressionSet")
checkTrue(validObject(eset3))
## The ExpressionSet features should not have the data from the
## SummarizedExperiment rows if they are from GRangesList, but they
## should be empty and the same length as the number of ranges.
checkEquals(unname(NROW(featureData(eset3))),
unname(length(rowRanges(rseList[[2]]))))
data("sample.ExpressionSet", package = "Biobase")
eset4 <- sample.ExpressionSet
eset5 <- as(as(eset4, "RangedSummarizedExperiment"), "ExpressionSet")
checkTrue(validObject(eset5))
## this is necessary because the order in environments is undefined.
compareLists <- function(x, y) {
nmsX <- names(x)
nmsY <- names(y)
reorderY <- match(nmsY, nmsX)
checkIdentical(x, y[reorderY])
}
compareLists(as.list(assayData(eset4)),
as.list(assayData(eset5)))
checkIdentical(experimentData(eset4),
experimentData(eset5))
checkIdentical(annotation(eset4),
annotation(eset5))
checkIdentical(protocolData(eset4),
protocolData(eset5))
checkIdentical(featureNames(eset4),
featureNames(eset5))
checkIdentical(sampleNames(eset4),
sampleNames(eset5))
}
test_GenomicRanges_SummarizedExperiment_coercion_lockedEnvironment <- function()
{
## https://github.com/Bioconductor/SummarizedExperiment/issues/43
se = SummarizedExperiment(list(exprs = matrix(1:10, 5)))
es1 = es2 = as(se, "ExpressionSet")
original <- exprs(es2)
checkIdentical(original, exprs(es2))
exprs(es1)[1, 1] = 2
checkTrue(!identical(original, exprs(es1)))
checkIdentical(original, exprs(es2))
}
test_GenomicRanges_SummarizedExperiment_coercion_mappingFunctions <- function()
{
DEACTIVATED("Skip test needing unpackaged database")
## naiveRangeMapper
## valid object from empty object
checkTrue(validObject(makeSummarizedExperimentFromExpressionSet(ExpressionSet())))
## valid object from sample ExpressionSet
data("sample.ExpressionSet", package = "Biobase")
eset1 <- sample.ExpressionSet
checkTrue(validObject(makeSummarizedExperimentFromExpressionSet(eset1)))
## makeSummarizedExperimentFromExpressionSet should be the same as `as`
## with default args
checkEquals(makeSummarizedExperimentFromExpressionSet(eset1),
as(eset1, "RangedSummarizedExperiment"))
## probeRangeMapper
## valid object from empty object
checkTrue(validObject(
makeSummarizedExperimentFromExpressionSet(ExpressionSet(),
probeRangeMapper)))
## valid object from sample ExpressionSet
se1 <- makeSummarizedExperimentFromExpressionSet(eset1, probeRangeMapper)
checkTrue(validObject(se1))
## Granges returned have rownames that were from the featureNames
checkTrue(all(rownames(rowRanges(se1)) %in% featureNames(eset1)))
## geneRangeMapper
## valid object from empty object
checkTrue(validObject(
makeSummarizedExperimentFromExpressionSet(ExpressionSet(),
geneRangeMapper(NULL))))
## valid object from sample ExpressionSet
se2 <- makeSummarizedExperimentFromExpressionSet(eset1,
geneRangeMapper("TxDb.Hsapiens.UCSC.hg19.knownGene"))
checkTrue(validObject(se2))
## Granges returned have rownames that were from the featureNames
checkTrue(all(rownames(rowRanges(se2)) %in% featureNames(eset1)))
}
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