Just to mention that the issue with rowSums() on a big DelayedMatrix
objects that you are referring to Tim is duly noted and will be one
of my first priorities once we're done with the release process.
Cheers,
H.
On 04/30/2018 09:57 AM, Tim Triche, Jr. wrote:
much obliged -- and the packages are terrific, I am not surprised that a
big step is accompanied with some growing pains.
Thanks to you and Herve and Keegan for enthusiastically chasing down, and
spending your time fixing, this and other bugs.
Having fiddled with bigMemory and bigMatrix backends for
SummarizedExperiment over the years, I know how many kicks and stings exist
under the covers, and greatly appreciate your (plural) efforts.
--t
On Mon, Apr 30, 2018 at 12:30 PM, Peter Hickey <peter.hic...@gmail.com>
wrote:
Tim: As the developer of DelayedMatrixStats (and enthusiastic 'canary down
the coal mine' user-dev of DelayedArray) I'm obviously invested in reducing
the confusion around these packages
I'm going to write some blog posts-cum-vignettes-cum-F1000 around these
issues over the coming weeks, with the ultimate goal of improving the
packages themselves.
Pete
On Mon., 30 Apr. 2018, 12:11 pm Tim Triche, Jr., <tim.tri...@gmail.com>
wrote:
But if you merge methods like that, the error method can be that much more
difficult to identify. It took a couple of weeks to chase that bug down
properly, and it ended up down to rowMeans2 vs rowMeans.
I suppose the merged/abstracted method allows to centralize any such
dispatch into one place and swap out ill-behaved methods once identified,
so as long as DelayedArray/DelayedMatrixStats quirks are
documented/understood, maybe it is better to create this union class?
The Matrix/matrixStats/DelayedMatrix/DelayedMatrixStats situation has
been
"interesting" in practical terms, as seemingly simple abstractions appear
to require more thought. That was my only point.
--t
On Mon, Apr 30, 2018 at 11:28 AM, Martin Morgan <
martin.mor...@roswellpark.org> wrote:
But that issue will be fixed, so Tim's advice is inappropriate.
On 04/30/2018 10:42 AM, Tim Triche, Jr. wrote:
Don't do that. Seriously, just don't.
https://urldefense.proofpoint.com/v2/url?u=https-3A__github.com_Bioconductor_DelayedArray_issues_16&d=DwIFaQ&c=eRAMFD45gAfqt84VtBcfhQ&r=BK7q3XeAvimeWdGbWY_wJYbW0WYiZvSXAJJKaaPhzWA&m=WCuDvGWmDrT5ZoYylftzjbrlaEu-lOxIIJaNJgn6itQ&s=kC-1EPn1Q-IuXzwk3-l-pJNp8zu4tXBnAP-1VPWKlbs&e=
--t
On Mon, Apr 30, 2018 at 10:02 AM, Elizabeth Purdom <
epur...@stat.berkeley.edu> wrote:
Hello,
I am trying to extend my package to handle `HDF5Matrix` class ( or
more
generally `DelayedArray`). I currently have S4 functions for `matrix`
class. Usually I have a method for `SummarizedExperiment`, which will
call
call the method on `assay(x)` and I want the method to be able to deal
with
if `assay(x)` is a `DelayedArray`.
Most of my functions, however, do not require separate code depending
on
whether `x` is a `matrix` or `DelayedArray`. They are making use of
existing functions that will make that choice for me, e.g. rowMeans or
subsetting. My goal right now is compatibility, not cleverness, and
I'm
not
creating HDF5 methods to handle other cases. (If something doesn't
currently exist, then I just enclose `x` with `data.matrix` or
`as.matrix`
and call the matrix into memory — for cleanliness and ease in updating
with
appropriate methods in future, I could make separate S4 functions for
these
specific tasks to dispatch, but that's outside of the scope of my
question). So for simplicity assume I don't really need to dispatch
*my
code* -- that the methods I'm going to use do that.
The natural solution for me seem to use `setClassUnion` and I was
wondering if such a virtual class already exists? Or is there a better
way
to handle this?
Here's a simple example, using `rowMeans` as my example:
```
setGeneric("myNewRowMeans", function(x,...) { standardGeneric("
myNewRowMeans")})
setClassUnion("matrixOrDelayed",members=c("matrix", "DelayedArray"))
#' @importFrom DelayedArray rowMeans
setMethod("myNewRowMeans",
signature = "matrixOrDelayed",
definition = function(x,...){
# a lot of code independent of x
print("This is a lot of code shared
regardless
of
class of x\n")
# a lot of code that depends on x, but is
dispatched by the functions called
out<-rowMeans(x)
#a lot of code based on output of out
out<-out+1
return(out)
}
)
```
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--
Hervé Pagès
Program in Computational Biology
Division of Public Health Sciences
Fred Hutchinson Cancer Research Center
1100 Fairview Ave. N, M1-B514
P.O. Box 19024
Seattle, WA 98109-1024
E-mail: hpa...@fredhutch.org
Phone: (206) 667-5791
Fax: (206) 667-1319
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