[Bioc-devel] EXTERNAL: MultiAssayExperiment silently converting RangedSummarizedExperiments into SummarizedExperiments.

[Marcel Ramos]

Hi Charles,

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:

``` r
suppressPackageStartupMessages({
    library(SummarizedExperiment)
})
example(SummarizedExperiment, echo = FALSE)
mylist <- list(exo1 = rse, exo2 = se0)

simple <- as(mylist, "SimpleList")

simple[[1]]
#> class: SummarizedExperiment
#> dim: 200 6
#> metadata(0):
#> 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
package](https://reprex.tidyverse.org) (v0.3.0)</sup>

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.

- Marcel



On 8/28/19 1:28 AM, Charles Plessy wrote:
> Hello,
>
> 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 
> SummarizedExperiment.
>
> Here is a toy example to reproduce the issue:
>
> ```{r}
> library("MultiAssayExperiment")
> (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[[1]]   <- m[[1]])
> m # No change
> (m        <- c(m, exp2=SE))
> (m[[1]]   <- m[[1]])
> m # RangedSummarizedExperiment replaced with SummarizedExperiment
> sessionInfo()
> ```
>
> Am I misusing the MultiAssayExperiment objects, or is this a bug ?
>
> Have a nice day,
>
> Charles
>


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