On Mar 12, 2015, at 9:24 AM, Martin Morgan <mtmorgan at fredhutch.org> wrote:
On 03/12/2015 08:12 AM, Tim Triche, Jr. wrote:
What he said
This doesn't make any sense from an API perspective. When would a user ever expect to see unnamed assay matrices?
When there's a single assay?
On Mar 12, 2015, at 7:46 AM, Kasper Daniel Hansen <kasperdanielhansen at gmail.com> wrote:
allowing positional matching strikes me as being far too fragile.
Depending on the actual implementation, it may not even be clear there is
an order of the assays.
On Wed, Mar 11, 2015 at 2:45 PM, Valerie Obenchain <vobencha at fredhutch.org>
wrote:
Hi,
After talking with others the vote was against enforcing names on assays()
and for positional matching if all names are NULL. A mixture of names and
NULL throws an error.
example(SummarizedExperiment)
## all named
se2 = se1
assays(cbind(se1, se2))
List of length 1
names(1): counts
## mixture of names and NULL -> error
names(assays(se1)) = NULL
assays(cbind(se1, se2))
Error in assays(cbind(se1, se2)) :
error in evaluating the argument 'x' in selecting a method for function
'assays': Error in .bind.arrays(args, cbind, "assays") :
elements in ?assays? must have the same names
## all NULL -> positional matching
names(assays(se2)) = NULL
assays(cbind(se1, se2))
List of length 1
If we find common use cases where positional matching is needed with a
mixture of names and NULL we can always relax this constraint.
Changes are in 1.19.46.
Valerie
On 03/06/2015 08:20 AM, Valerie Obenchain wrote:
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.
List of length 1
names(1): counts1
List of length 1
names(1): counts2
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
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