Hi all,
I got a bit of weird behaviour with SummarizedExperiments in Bioc 3.6 and 3.7. I suppose it is a bug, but I might be wrong, since the accession to the SummarizedExperiment object is not really straight forward. Any suggestions? library(GenomicRanges) library(SummarizedExperiment) nrows <- 200; ncols <- 6 counts <- matrix(runif(nrows * ncols, 1, 1e4), nrows) colnames(counts) <- LETTERS[1:6] rownames(counts) <- 1:nrows counts2 <- counts-floor(counts) rowRanges <- GRanges(rep(c("chr1", "chr2"), c(50, 150)), IRanges(floor(runif(200, 1e5, 1e6)), width=100), strand=sample(c("+", "-"), 200, TRUE), feature_id=sprintf("ID%03d", 1:200)) colData <- DataFrame(Treatment=rep(c("ChIP", "Input"), 3), row.names=LETTERS[1:6]) se <- SummarizedExperiment(assays=list(counts=counts), rowRanges=rowRanges, colData=colData) colData(se)$xyz <- rep("",ncol(se)) metadata(se) <- list("meep" = "meep") str(metadata(se)) colData(se[, 1])$xyz <- "abc" str(metadata(se)) The first metadata() returns a list, length of 1, with the correct data. The second call returns a list of two, with a duplicated entries and every further colData modification (and replacing data) duplicates the entries in the metadata further. > str(metadata(se)) List of 1 $ meep: chr "meep" > colData(se[, 1])$xyz <- "abc" > str(metadata(se)) List of 2 $ meep: chr "meep" $ meep: chr "meep" > colData(se[, 2])$xyz <- "abc" > str(metadata(se)) List of 4 $ meep: chr "meep" $ meep: chr "meep" $ meep: chr "meep" $ meep: chr "meep" > colData(se[, 2])$xyz <- "abc" > str(metadata(se)) List of 8 $ meep: chr "meep" $ meep: chr "meep" $ meep: chr "meep" $ meep: chr "meep" $ meep: chr "meep" $ meep: chr "meep" $ meep: chr "meep" $ meep: chr "meep" Thanks for any advice and suggestions. Felix --- Felix Ernst, PhD Universit� Libre de Bruxelles RNA MOLECULAR BIOLOGY BIOPARK Charleroi Brussels-South CAMPUS Rue Profs Jeener & Brachet, 12 B-6041 Charleroi - Gosselies BELGIUM +32(2)650 9774 (office phone) <mailto:felix.er...@ulb.ac.be> felix.er...@ulb.ac.be [[alternative HTML version deleted]]
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