Thanks, I've exported it now from BiocGenerics. It shouldn't cause a duplication.
Michael On Mon, Dec 2, 2013 at 12:12 PM, Robert Castelo <robert.cast...@upf.edu>wrote: > 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>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 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
