hi Michael, thanks for your quick response, comments below.. On 12/2/13 6:29 PM, Michael Lawrence wrote: > A DataFrame being a SimpleList, coercion to list is immediate, so just > coerce to a list instead of a data.frame. > > do.call(pmax, as.list(DataFrame(x=1:10,y=2:11))) > thanks for tip, so i understand this route does not duplicate the object in memory, right?
> I added a do.call method in IRanges that does this for you. > that's great, i think however the new do.call() method still needs to be exported: library(IRanges) do.call(pmax, DataFrame(x=1:10, y=2:11)) Error in do.call(pmax, DataFrame(x = 1:10, y = 2:11)) : second argument must be a list IRanges::do.call(pmax, DataFrame(x=1:10, y=2:11)) Error: 'do.call' is not an exported object from 'namespace:IRanges' sessionInfo() R Under development (unstable) (2013-10-23 r64103) Platform: x86_64-apple-darwin12.5.0 (64-bit) locale: [1] en_US.UTF-8/en_US.UTF-8/en_US.UTF-8/C/en_US.UTF-8/en_US.UTF-8 attached base packages: [1] parallel stats graphics grDevices utils datasets methods [8] base other attached packages: [1] IRanges_1.21.13 BiocGenerics_0.9.1 loaded via a namespace (and not attached): [1] stats4_3.1.0 robert. > > > On Mon, Dec 2, 2013 at 8:58 AM, Robert Castelo <robert.cast...@upf.edu > <mailto:robert.cast...@upf.edu>> wrote: > > hi, > > i would like to do the following: > > library(IRanges) > > do.call(pmax, data.frame(x=1:10, y=2:11)) > [1] 2 3 4 5 6 7 8 9 10 11 > > with 'DataFrame' objects: > > do.call(pmax, DataFrame(x=1:10, y=2:11)) > Error in do.call(pmax, DataFrame(x = 1:10, y = 2:11)) : > second argument must be a list > > concretely with the metadata columns of GRanges objects, which are > DataFrame objects. > > currently i can do it by coercing back to DataFrame: > > do.call(pmax, as.data.frame(DataFrame(x=1:10, y=2:11))) > [1] 2 3 4 5 6 7 8 9 10 11 > > but if the GRanges object is large this becomes a significant > overhead in cpu and memory which i guess could be avoided by a > pmax method working on DataFrame objects directly. > > > thanks!! > robert. > ps: sessionInfo() > R Under development (unstable) (2013-10-20 r64082) > Platform: x86_64-unknown-linux-gnu (64-bit) > > locale: > [1] LC_CTYPE=en_US.UTF8 LC_NUMERIC=C > [3] LC_TIME=en_US.UTF8 LC_COLLATE=en_US.UTF8 > [5] LC_MONETARY=en_US.UTF8 LC_MESSAGES=en_US.UTF8 > [7] LC_PAPER=en_US.UTF8 LC_NAME=C > [9] LC_ADDRESS=C LC_TELEPHONE=C > [11] LC_MEASUREMENT=en_US.UTF8 LC_IDENTIFICATION=C > > attached base packages: > [1] parallel stats graphics grDevices utils datasets methods > [8] base > > other attached packages: > [1] IRanges_1.21.10 BiocGenerics_0.9.0 vimcom_0.9-91 setwidth_1.0-3 > [5] colorout_1.0-1 > > loaded via a namespace (and not attached): > [1] stats4_3.1.0 tools_3.1.0 > > _______________________________________________ > Bioc-devel@r-project.org <mailto:Bioc-devel@r-project.org> mailing > list > https://stat.ethz.ch/mailman/listinfo/bioc-devel > > [[alternative HTML version deleted]] _______________________________________________ Bioc-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/bioc-devel
