[Bioc-devel] SummarizedExperiment exptData() patch
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
Herv? Pag?s 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: hpages at fredhutch.org Phone: (206) 667-5791 Fax: (206) 667-1319