On 03/12/2014 03:02 PM, 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$tissue %in% c(“guts”, “brains”)]
x = droplevels(x)
vs. x$tissue = droplevels(x$tissue)
- a ‘droplevels’ argument (default: FALSE)
x = x[, x$tissue %in% c(“guts”, “brains”), droplevels=TRUE]
there are a surprising number of places were levels could be dropped -- each
column of colData, each column of (possibly two levels of) 'mcols' on the row
data, and the seqlevels of the row data.
Does this make sense lower in the class hierarchy, e.g., Vector, as well as
GRanges/List?
Martin
Wolfgang
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