[Bioc-devel] requirement for named assays in SummarizedExperiment

Hi Aaron,

Thanks for catching this.

I favor enforcing names in 'assays'. Combining by position alone is too
dangerous. I'm thinking of the VCF class where the genome information is
stored in 'assays' and the fields are rarely in the same order.

Looks like we also need a more informative error message when names
don't match.

 > assays(se1)

List of length 1
names(1): counts1

 > assays(se2)

List of length 1
names(1): counts2

 > cbind(se1, se2)

Error in sQuote(accessorName) :
   argument "accessorName" is missing, with no default


Valerie


On 03/05/2015 11:09 PM, Aaron Lun wrote:

Dear all,

I stumbled upon some unexpected behaviour with cbind'ing
SummarizedExperiment objects with unnamed assays:

require(GenomicRanges)
nrows <- 5; ncols <- 4
counts <- matrix(runif(nrows * ncols, 1, 1e4), nrows)
rowData <- GRanges("chr1", IRanges(1:nrows, 1:nrows))
colData <- DataFrame(Treatment=1:ncols, row.names=LETTERS[1:ncols])
sset <- SummarizedExperiment(counts, rowData=rowData, colData=colData)
sset

class: SummarizedExperiment
dim: 5 4
exptData(0):
assays(1): ''
rownames: NULL
rowData metadata column names(0):
colnames(4): A B C D
colData names(1): Treatment

cbind(sset, sset)

dim: 5 8
exptData(0):
assays(0):
rownames: NULL
rowData metadata column names(0):
colnames(8): A B ... C1 D1
colData names(1): Treatment

Upon cbind'ing, the assays in the SE object are lost. I think this is
due to the fact that the cbind code matches up assays by their names.
Thus, if there are no names, the code assumes that there are no assays.

I guess this could be prevented by enforcing naming of assays in the
SummarizedExperiment constructor. Or, the binding code could be modified
to work positionally when there are no assay names, e.g., by cbind'ing
the first assays across all SE objects, then the second assays, etc.

Any thoughts?

Regards,

Aaron

sessionInfo()

R Under development (unstable) (2014-12-14 r67167)
Platform: x86_64-unknown-linux-gnu (64-bit)

locale:
  [1] LC_CTYPE=en_US.UTF-8       LC_NUMERIC=C
  [3] LC_TIME=en_US.UTF-8        LC_COLLATE=en_US.UTF-8
  [5] LC_MONETARY=en_US.UTF-8    LC_MESSAGES=en_US.UTF-8
  [7] LC_PAPER=en_US.UTF-8       LC_NAME=C
  [9] LC_ADDRESS=C               LC_TELEPHONE=C
[11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C

attached base packages:
[1] stats4    parallel  stats     graphics  grDevices utils
datasets
[8] methods   base

other attached packages:
[1] GenomicRanges_1.19.42 GenomeInfoDb_1.3.13   IRanges_2.1.41
[4] S4Vectors_0.5.21      BiocGenerics_0.13.6

loaded via a namespace (and not attached):
[1] XVector_0.7.4