Is that a good thing? (such an important special case that slapping a name on
what exactly the assay contains would break other functionality?)
If memory serves, the shallow reference class that points at the assays doesn't
need to copy objects in order for them to have a name, but maybe my me
Yes, a single-assay SummarizedExperiment would be the most common case
for unnamed assays. But I think at the very least there should be a
warning on unnamed assays.
On 3/12/15 9:24 AM, Martin Morgan wrote:
On 03/12/2015 08:12 AM, Tim Triche, Jr. wrote:
What he said
This doesn't make any sen
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?
--t
On Mar 12, 2015, at 7:46 AM, Kasper Daniel Hansen
wrote:
allowing positional
What he said
This doesn't make any sense from an API perspective. When would a user ever
expect to see unnamed assay matrices?
--t
> On Mar 12, 2015, at 7:46 AM, Kasper Daniel Hansen
> wrote:
>
> allowing positional matching strikes me as being far too fragile.
> Depending on the actual imp
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
wrote:
> Hi,
>
> After talking with others the vote was against enforcing names o
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
#
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 erro
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 <- DataF
