Hi Ludwig,
Excellent catch! Thanks for the report.
This should be fixed in SummarizedExperiment release (1.6.4) and devel
(1.7.7).
Cheers,
H.
On 09/13/2017 02:54 PM, Ludwig Geistlinger wrote:
Coercing vice versa, i.e. from SummarizedExperiment to ExpressionSet,
which is defined in
SummarizedExperiment/R/makeSummarizedExperimentFromExpressionSet.R
as follows:
setAs("SummarizedExperiment", "ExpressionSet", function(from)
as(as(from, "RangedSummarizedExperiment"), "ExpressionSet")
)
also seems to be a bit problematic, as it makes you lose your rowData/fData.
Here is an example:
## Constructing the SE similar to examples of ?SummarizedExperiment
nrows <- 200; ncols <- 6
counts <- matrix(runif(nrows * ncols, 1, 1e4), nrows)
colData <- DataFrame(Treatment=rep(c("ChIP", "Input"), 3),
row.names=LETTERS[1:6])
## some rowData with simulated gene IDs
rowData <- DataFrame(EntrezID=sample(1000, 200), row.names=paste0("g",
1:200))
se <- SummarizedExperiment(assays=SimpleList(exprs=counts),
colData=colData, rowData=rowData)
# this is how it looks
rowData(se)
DataFrame with 200 rows and 1 column
EntrezID
<integer>
1 289
2 476
3 608
4 998
5 684
... ...
196 331
197 590
198 445
199 95
200 129
(why did I actually lost the rownames g1-g200 here?)
## Coercing to Expression makes me losing the rowData/fData
eset <- as(se, "ExpressionSet")
fData(eset)
data frame with 0 columns and 200 rows
## So where is the problem?
## Apparently in the coercion
## from SummarizedExperiment to RangedSummarizedExperiment
rse <- as(se, "RangedSummarizedExperiment")
rowData(rse)
DataFrame with 200 rows and 0 columns
--
Hervé Pagès
Program in Computational Biology
Division of Public Health Sciences
Fred Hutchinson Cancer Research Center
1100 Fairview Ave. N, M1-B514
P.O. Box 19024
Seattle, WA 98109-1024
E-mail: hpa...@fredhutch.org
Phone: (206) 667-5791
Fax: (206) 667-1319
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