Unlike exptData(), metadata() returns an ordinary list. These methods
also need to be exported and have aliases in the man page for
RangedSummarizedExperiment. I'll add something like that to the
SummarizedExperiment package. Thanks Tim!
H.
On 05/12/2015 11:27 AM, Tim Triche, Jr. wrote:
one setMethod and a setReplaceMethod later, all seems to be well...
## testing:
library(SummarizedExperiment)
nrows <- 200; ncols <- 6
counts <- matrix(runif(nrows * ncols, 1, 1e4), nrows)
rowRanges <- GRanges(rep(c("chr1", "chr2"), c(50, 150)),
IRanges(floor(runif(200, 1e5, 1e6)), width=100),
strand=sample(c("+", "-"), 200, TRUE))
colData <- DataFrame(Treatment=rep(c("ChIP", "Input"), 3),
row.names=LETTERS[1:6])
sset <- SummarizedExperiment(assays=SimpleList(counts=counts),
rowRanges=rowRanges, colData=colData)
## now futz with it
exptData(sset) <- List(foo='bar')
identical(metadata(sset), exptData(sset))
## TRUE
Works for my purposes...
Timothy J. Triche, Jr., PhD
Jane Anne Nohl Division of Hematology
USC/Norris Comprehensive Cancer Center
Harlyne Norris Research Tower, room 3509
--
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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