Error when subsetting features from a `SingleCellExperiment` object from `experiments(x)`

[cvanderaa]

Hello, I encounter an error when I subset features from a SingleCellExperiment object that is contained in a MultiAssayExperiment object. I want to perform this by subsetting the output of experiments(x) which (from the traceback()) calls to subset_List_by_List. Note it works perfectly fine for a SummarizedExperiment object.

Here is some reproducible example:

## Create a mock expression matrix
matrix(1:100, 10) %>%
  `rownames<-`(letters[1:10]) %>%
  `colnames<-`(LETTERS[1:10]) -> exprs
## Build SE and SCE objects for comparison 
se <- SummarizedExperiment(SimpleList(exprs))
sce <- SingleCellExperiment(SimpleList(exprs))
## Build the MAE object containing the SE and SCE as assays
mae <- MultiAssayExperiment(ExperimentList(se = se, 
                                           sce = sce))

## Subsetting works fine for SE
experiments(mae)[list(se = "a")]
## ExperimentList class object of length 1:
##  [1] se: SummarizedExperiment with 1 rows and 10 columns

## Error with SCE
experiments(mae)[list(sce = "a")]
## Error in .wrap_in_length_one_list_like_object(value, names(x)[[i]], x) : 
##   failed to coerce 'list(value)' to a ExperimentList object of length 1

[LiNk-NY]

Hi @cvanderaa We don't have explicit methods for ExperimentList so any [ subsetting will use the List methods and those probably are not meant to handle the input. I can look into adding an explicit [ method for ExperimentList. There are a couple of alternatives in the meantime:

## Use MAE-level subsetting
mae[list(sce = "a"), ]

## Use subsetByRow method for ExperimentList
subsetByRow(experiments(mae), list(sce = "a"))

[lwaldron]

@cvanderaa what do you want experiments(mae)[list(sce = "a")] to do? Is it this?

> subsetByRow(experiments(mae), "a") %>% subsetByAssay(., "sce")
ExperimentList class object of length 1:
 [1] sce: SingleCellExperiment with 1 rows and 10 columns

[cvanderaa]

Thank you for your answers @LiNk-NY and @lwaldron. My goal is to include and use SingleCellExperiment objects in a Features object that is based on your MultiAssayExperiment class. Features (developed by @lgatto) integrates various levels of linked proteomic expression data (e.g. proteins expression levels computed from peptide expression levels). I want to adapt Features for single-cell proteomics usage.

One very interesting functionality of Features is to subset, let's say, a protein over all levels of expression, typically PSM, peptide and protein. Of course in my reproducible example, it is strange to have a list with only 1 entry, but a real case scenario would look like this:

experiments(mae)[list(PSM = c("psm1", "psm2" , "psm3", "psm4"),
                      peptide = c("peptide1", "peptide2"), 
                      protein = c("protein1"))]

See this line in Features where the error occurs. featurename_list is a list as given in the code chunk above.

Since this works perfectly for SummarizedExperiments, I was hoping it would be possible to make it also work for SingleCellExperiments without too much effort.

[cvanderaa]

Sorry, don't mind my last comment, I was able to adapt Features to solve the issue with the solution of @LiNk-NY

experiments(x[list(sce = "a"), ])    

Thanks again for your help!

[lwaldron]

I do think row subsetting should be supported for ExperimentList, and it is when using subsetByRow(). @LiNk-NY I would propose that the following should be equivalent (and should be documented in ?ExperimentList-class and the cheatsheet).

 subsetByRow(experiments(mae), "a")
ExperimentList class object of length 2:
 [1] se: SummarizedExperiment with 1 rows and 10 columns
 [2] sce: SingleCellExperiment with 1 rows and 10 columns
> experiments(mae)["a", ]
Error: subscript contains invalid names
>

[stale[bot]]

This issue has been automatically marked as stale because it has not had any recent activity. It will be closed if no further activity occurs. Thank you for your contributions.

[LiNk-NY]

You can test in this branch: https://github.com/waldronlab/MultiAssayExperiment/tree/expsubset

[stale[bot]]

This issue has been automatically marked as stale because it has not had any recent activity. It will be closed if no further activity occurs. Thank you for your contributions.

[hpages]

Hi,

FWIW the root of the problem reported by the OP was a bug in the SingleCellExperiment class that got fixed 9 days ago: https://github.com/drisso/SingleCellExperiment/commit/bc220cab41b7112347dda5e094ebb2a9c987fb23 This was a bug in the extractROWS() method for SingleCellExperiment objects. The bug was breaking things based on extractROWS() like head(sce, n=2) or experiments(mae)[list(sce="a")].

Note that changing the behavior of subsetting on ExperimentList objects was not needed in order to address the problem.

H.