yes, if a formal extension is warranted. the metadata slot could also be used.
On Thu, Jun 18, 2015 at 2:59 PM, Kasper Daniel Hansen < kasperdanielhan...@gmail.com> wrote: > I think the more clean solution for Davide (if he inists on having separate > objects; I decided against it in minfi) is to extend the class to allow > this. > > Kasper > > On Thu, Jun 18, 2015 at 12:25 AM, Ryan <r...@thompsonclan.org> wrote: > > > Oh wow, I didn't know you could put a DataFrame into a single column of > > another DataFrame. That actually solves a problem for me too (I don't > > intend to expose nested DataFrames to the users though). > > > > > > On 6/17/15 7:23 PM, Martin Morgan wrote: > > > >> On 06/17/2015 11:41 AM, davide risso wrote: > >> > >>> Dear list, > >>> > >>> I'm creating an R package to store RNA-seq data of a somewhat large > >>> project > >>> in which I'm involved. > >>> > >>> One of the initial goals is to compare different pre-processing > >>> pipelines, > >>> hence I have multiple expression matrices corresponding to the same > >>> samples. > >>> The SummarizedExperiment class seems a good candidate, since I have > >>> multiple expression matrices with the same rowData and colData > >>> information. > >>> > >>> I have several sample-specific variables that I want to store with the > >>> object, namely, experimental information (e.g., batch, date, > experimental > >>> condition, ...) and sample quality (e.g., proportion of aligned reads, > >>> total duplicate reads, etc...). > >>> > >>> Of course, I can always create one big data frame concatenating the two > >>> (experimental info + sample quality), but it seems that both > conceptually > >>> and practically, it might be useful to have two separate data frames. > >>> Since this seems somewhat a reasonably standard type of information > that > >>> one would want to carry on, I was wondering if it would be possible / > >>> useful to allow the user to have multiple data.frames in the colData > slot > >>> > >> > >> Actually, colData() is a DataFrame, and a DataFrame column can contain a > >> DataFrame. So after > >> > >> example(SummarizedExperiment) > >> > >> we could make some faux sample quality data > >> > >> quality = DataFrame(x=1:6, y=6:1, row.names=colnames(se1)) > >> > >> add this as a column in the colData() > >> > >> colData(se1)$quality = quality > >> > >> (or create the SummarizedExperiment from a similar DataFrame up-front) > >> and manage our grouped data > >> > >> > colData(se1) > >> DataFrame with 6 rows and 2 columns > >> Treatment quality > >> <character> <DataFrame> > >> A ChIP ######## > >> B Input ######## > >> C ChIP ######## > >> D Input ######## > >> E ChIP ######## > >> F Input ######## > >> > colData(se1[,1:2])$quality > >> DataFrame with 2 rows and 2 columns > >> x y > >> <integer> <integer> > >> A 1 6 > >> B 2 5 > >> > >> I'm not sure that this is any less confusing to the end user than having > >> to manage a DataFrameList(), but it does not require any new features. > >> > >> Martin > >> > >> of SummarizedExperiment. > >>> > >>> Best, > >>> Davide > >>> > >>> [[alternative HTML version deleted]] > >>> > >>> _______________________________________________ > >>> Bioc-devel@r-project.org mailing list > >>> https://stat.ethz.ch/mailman/listinfo/bioc-devel > >>> > >>> > >> > >> > > _______________________________________________ > > 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 > [[alternative HTML version deleted]] _______________________________________________ Bioc-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/bioc-devel