[Bioc-devel] do SummarizedExperiments really need colnames?

[Morgan, Martin]

Thanks Peter and Aaron.

For SummarizedExperiment 1.1.9 in svn now:

For Aaron's original issue, SummarizedExperiment now allows construction from NULL colnames; it does not construct colnames.

The behavior of SummarizedExperiment with respect to colnames is to use and keep them if provided, but not to add colnames to assays if they are absent -- they are provided in the constructor to se2, so present in the assay in se2.

The inconsistency between assay colnames and colData rownames in the constrution of se3 is now (and should have been before) an error.

> assay = matrix(0, 2, 3, dimnames=list(NULL, LETTERS[1:3]))
> colData = DataFrame(row.names=letters[1:3])
> SummarizedExperiment(assay, colData=colData)
Error in FUN(X[[i]], ...) : 
  assay colnames() must be NULL or equal colData rownames()

Thanks for the feed back / bug reports; please let me know if there are additional issues.
________________________________________
From: Peter Hickey [peter.hickey at gmail.com]
Sent: Sunday, December 06, 2015 7:56 PM
To: Morgan, Martin
Cc: alun at wehi.edu.au; bioc-devel at r-project.org
Subject: Re: do SummarizedExperiments really need colnames?

While on the topic of SummarizedExperiment colnames, the circumstances in which these are stripped from the assays and overridden by colData is confusing to me, particularly case 2 below (a warning in case 3 might be useful too).

> m1 <- matrix(1:10, ncol = 2)
> m2 <- m1
> colnames(m2) <- c("A", "B")
>
> se1 <- SummarizedExperiment(m1, colData = DataFrame(row.names = c("A", "B")))
> se2 <- SummarizedExperiment(m2)
> se3 <- SummarizedExperiment(m2, colData = DataFrame(row.names = c("C", "D")))
>
> # colnames correctly set to c("A", "B") and stripped from assays
> colnames(se1)
[1] "A" "B"
> se1 at assays[[1]]
[,1] [,2]
[1,] 1 6
[2,] 2 7
[3,] 3 8
[4,] 4 9
[5,] 5 10
> # colnames correctly set to c("A", "B") set and but not stripped from assays
> colnames(se2)
[1] "A" "B"
> se2 at assays[[1]]
A B
[1,] 1 6
[2,] 2 7
[3,] 3 8
[4,] 4 9
[5,] 5 10
> # colnames set to c("C", "D") (without warning about mismatch) and stripped
> # from assays
> se3 at assays[[1]]
[,1] [,2]
[1,] 1 6
[2,] 2 7
[3,] 3 8
[4,] 4 9
[5,] 5 10

> sessionInfo()
R Under development (unstable) (2015-11-28 r69714)
Platform: x86_64-apple-darwin13.4.0 (64-bit)
Running under: OS X 10.10.5 (Yosemite)

locale:
[1] en_AU.UTF-8/en_AU.UTF-8/en_AU.UTF-8/C/en_AU.UTF-8/en_AU.UTF-8

attached base packages:
[1] stats4 parallel stats graphics grDevices utils datasets
[8] methods base

other attached packages:
[1] SummarizedExperiment_1.1.5 Biobase_2.31.1
[3] GenomicRanges_1.23.4 GenomeInfoDb_1.7.3
[5] IRanges_2.5.9 S4Vectors_0.9.11
[7] BiocGenerics_0.17.2

loaded via a namespace (and not attached):
[1] zlibbioc_1.17.0 XVector_0.11.1



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