I would prefer the droplevels method for SummarizedExperiment, since
this is consistent with the use of droplevels on data.frame objects.
On Wed 12 Mar 2014 03:02:37 PM PDT, Wolfgang Huber wrote:
Hi Martin, Mike
a DESeq2 user brought up the observation that when he subsets a ‘DESeqDataSet’
object (the class inherits from ‘SummarizedExperiment’) by samples, he often
ends up with unused factor levels in the colData. (Esp. since the subsetting is
often to select certain subgroups). Would either of the following two make
sense:
- a ‘droplevels’ method for ‘SummarizedExperiment’ that efficiently and
conveniently removes unused levels, i.e.
x = x[, x$tissue %in% c(“guts”, “brains”)]
x = droplevels(x)
- a ‘droplevels’ argument (default: FALSE)
x = x[, x$tissue %in% c(“guts”, “brains”), droplevels=TRUE]
Wolfgang
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