[Bioc-devel] EXTERNAL: MultiAssayExperiment silently converting RangedSummarizedExperiments into SummarizedExperiments.
M@rce|@R@mo@ @end|ng |rom ro@we||p@rk@org
Wed Sep 4 00:03:20 CEST 2019
Thank you for your post and for providing a reproducible example.
I was able to reduce the example to behavior from the coerce method on
`list`/`ANY` objects to `SimpleList`.
Here is the reduced example:
example(SummarizedExperiment, echo = FALSE)
mylist <- list(exo1 = rse, exo2 = se0)
simple <- as(mylist, "SimpleList")
#> class: SummarizedExperiment
#> dim: 200 6
#> assays(1): counts
#> rownames: NULL
#> rowData names(1): feature_id
#> colnames(6): A B ... E F
#> colData names(1): Treatment
vapply(simple, class, character(1L))
#> exo1 exo2
#> "SummarizedExperiment" "SummarizedExperiment"
<sup>Created on 2019-09-03 by the [reprex
It appears that `S4Vectors:::coerceToSimpleList` looks for the
`S4Vectors:::lowestListElementClass` and coerces all classes in the list
to be the base `SummarizedExperiment` class. I'm not sure what the
reasoning is behind the behavior.
Can you chime in Hervé? Thanks.
On 8/28/19 1:28 AM, Charles Plessy wrote:
> I am using MultiAssayExperiment as a base class in the CAGEr package.
> In Bioconductor 3.10, CAGEr is broken because updates of
> RangeSummarizedExperiment experiments trigger their silent conversion
> to SummarizedExperiment objects (basically discarding the ranges). This
> only happens when there is another experiment slot that contains a plain
> Here is a toy example to reproduce the issue:
> (DF <- DataFrame(sample1=c(1,2), sample2=c(1,3)))
> (rRanges <- GPos("chr1", 1:2, "+"))
> (cData <- DataFrame(type=c("control", "treatment"), row.names =
> c("sample1", "sample2")))
> (rSE <- SummarizedExperiment(SimpleList(DF), rowRanges = rRanges,
> colData = cData))
> (SE <- SummarizedExperiment(SimpleList(DF), colData = cData))
> (m <- MultiAssayExperiment(ExperimentList(exp1=rSE)))
> (m[] <- m[])
> m # No change
> (m <- c(m, exp2=SE))
> (m[] <- m[])
> m # RangedSummarizedExperiment replaced with SummarizedExperiment
> Am I misusing the MultiAssayExperiment objects, or is this a bug ?
> Have a nice day,
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