[Bioc-devel] as.list.List (was Re: parallel package generics)
Martin, Great. Nice, and makes sense, and should be added to R/List-class But, but It is 'a good thing' that it make Reduce and mclapply 'work'... But, they work in an inefficient manner. Modifying base::Reduce and parallel::mclapply as I suggest (to NOT coerce to list at all) make them VERY MUCH faster. and does away with the need for BioC Generics Do you agree that these changes should be made in 'upstream' packages? --Malcolm
On 10/25/12 2:34 PM, "Martin Morgan" <mtmorgan at fhcrc.org> wrote:
On 10/25/2012 07:53 PM, Cook, Malcolm wrote:
Namely, base::Reduce coerces X to a list using as.list if it is an object whereas BiocGenerics::Reduce does not. Otherwise they are identical. As a result, base::Reduce(myGRangesList) fails with "no method for coercing this S4 class to a vector".
Well, so when you put it this way... I was wondering why there is no
as.list.List
i.e., an S3 method for List on the generic as.list? This seems to be
consistent
with the recommendation on ?Methods under 'Methods for S3 Generic
Functions'
(and this little hack seems to allow both Reduce and mclapply to 'work').
Index: NAMESPACE
===================================================================
--- NAMESPACE (revision 70700)
+++ NAMESPACE (working copy)
@@ -332,3 +332,4 @@
expand
)
+S3method(as.list, List)
Index: R/List-class.R
===================================================================
--- R/List-class.R (revision 70700)
+++ R/List-class.R (working copy)
@@ -442,10 +442,11 @@
### Coercion.
###
+as.list.List <-
+ function(x, ...) lapply(x, identity)
+
setAs("List", "list", function(from) as.list(from))
-setMethod("as.list", "List", function(x, ...) lapply(x, identity))
-
setGeneric("as.env", function(x, ...) standardGeneric("as.env"))
setMethod("as.env", "List",
--
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