On Fri, Mar 21, 2014 at 11:33 AM, Michael Lawrence <lawrence.michael at="" gene.com=""> wrote: > On Fri, Mar 21, 2014 at 11:05 AM, Steve Lianoglou > <lianoglou.steve at="" gene.com="">wrote: > >> Howdy, >> >> On Fri, Mar 21, 2014 at 9:12 AM, Michael Lawrence >> <lawrence.michael at="" gene.com=""> wrote: >> > Not really sure how ddply works (the "." syntax seems a bit weird) but I >> > think you want something like: >> > >> > do.call(c, tapply(gr, list(gr$transcript_id, gr$type), function(tt) { >> > }, simplify=FALSE)) >> >> Clever -- somehow I never realized we had specialized versions of more >> than just lapply, and mapply ... maybe it's because I've never been a >> fan of `tapply` (I mean, what does the `t` mean, anyway?) >> >> > I'm pretty sure it originates from its use in generating contingency > /t/ables, see example(tapply). > > >> Anyway, the OP's `ggply` function would be neat -- perhaps a `bioplyr` >> package could interesting/fun for somebody whose got some time for a >> little yak shaving ... ;-) >> >> > > I was thinking to achieve something close to the convenience of ddply > without moving too far from the R API would be: > > aggregate(~ transcript_id + type, gr, function(tt) { > }) `aggregate` ... Ack! My eyes! To my detriment (and embarrassment!), my eyes always begin to gloss-over when I try to parse that syntax[1] when it's used for things outside of linear modeling, and have always steered clear (although I am trying to make a more concerted effort of dealing with it in reshap-ing and stuff more recently). I know it's a base R thing ... but ugh ... I guess it should have clicked by now, but I've never given it its due, hence my love of plyr and data.table for (at least) these types of summary tasks. [1] Heaven forbid there be a call to `substitute` or `quote` in close proximity to a strange formula-like looking `aggregate` or `xtabs` call -- I may start seeing dead people. -steve -- Steve Lianoglou Computational Biologist Genentech