[Bioc-devel] SummarizedExperiment subset of 4 dimensions

[Jesper Gådin]

Hi!

The SummarizedExperiment class is an extremely powerful container for
biological data(thank you!), and all my thinking nowadays is just circling
around how to stuff it as effectively as possible.

Have been using 3 dimension for a long time, which has been very
successful. Now I also have a case for using 4 dimensions. Everything
seemed to work as expected until I tried to subset my object, see example.

library(GenomicRanges)

rowRanges <- GRanges(
                seqnames="chrx",
                ranges=IRanges(start=1:3,end=4:6),
                strand="*"
                )

coldata <- DataFrame(row.names=paste("s",1:3, sep=""))

assays <- SimpleList()

#two dim
assays[["dim2"]] <- array(0,dim=c(3,3))
se <- SummarizedExperiment(assays, rowRanges = rowRanges, colData=coldata)
se[1]
#works

#three dim
assays[["dim3"]] <- array(0,dim=c(3,3,3))
se <- SummarizedExperiment(assays, rowRanges = rowRanges, colData=coldata)
se[1]
#works

#four dim
assays[["dim4"]] <- array(0,dim=c(3,3,3,3))
se <- SummarizedExperiment(assays, rowRanges = rowRanges, colData=coldata)
se[1]
#does not work
#Error in x[i, , , drop = FALSE] : incorrect number of dimensions

This is also the case for rbind and cbind. Would it be appropriate to ask
you to update the SE functions to handle subset, rbind, cbind also for 4
dimensions? I know the time for next release is very soon, so maybe it is
better to wait until after April 16. Just let me know your thoughts about
it.

Jesper

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