SummarizedExperiment
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Bioconductor
SummarizedExperiment container
I've recently realised that if two objects have different rownames, `cbind()` does not seem to throw an error. Whereas `rbind()` does throws an error if colnames are different (the behaviour...
Consider the following example: ```r library(SummarizedExperiment) se
Coercing a subclass of an RSE to an SE discards the row names: ```r library(SummarizedExperiment) example(SummarizedExperiment, echo=FALSE) setClass("MyExperiment", contains="RangedSummarizedExperiment") me
``` library(SummarizedExperiment) mymat = matrix((1:6)*1.0, nc=3) dimnames(mymat) = list(c("A", "B"), letters[1:3]) se1 = SummarizedExperiment(mymat) validObject(se1) library(S4Vectors) ndf = DataFrame(v1=10:12) rownames(ndf) = letters[3:1] ndf colData(se1) = ndf newAa = assay(se1["A", "a"])...
Inspired by https://support.bioconductor.org/p/126722/. The problem is what to do when a `rowData` field is not identical across `cbind`'d elements. Currently `cbind` throws an error, which is understandable (and safest) but...
I would have assumed that `c()` would be equivalent to `rbind()` on SummarizedExperiment. However, it fails, because `bindROWS,Vector()` does not handle the assays. Perhaps `rbind,SummarizedExperiment()` should be refactored into a...
Hello, this is just a suggestion. If a have to SE, with the same data, but one has a metadata column that the other does not have. The package gives...
Hi Hervé, @hpages I have an example here: ```r library(GenomicRanges) library(SummarizedExperiment) example(GRanges) example(SummarizedExperiment) ss
`all.equal()` on SummarizedExperiment objects needs to perform a "deep comparison" in order to avoid false positives or false negatives. In particular this means that it must perform a deep comparison...
