Hi Patrick, I second Robert's thanks - reduce on RangedData is really useful. I have an additional suggestion (you might already be on the case with this one). I was trying to reduce a RangedData object that didn't have any strand/score/name, and kept getting an error (Error in endoapply(x[, by], FUN) : 'FUN' did not produce an endomorphism). I got around that by just adding a fake name (or strand or whatever) that is identical for all objects. It would be even nicer if reduce could handle bare bones RangedData objects without needing this workaround. Here is some code to show you what I mean, following your example: suppressMessages(library(IRanges)) sta <- c(1, 2, 5, 6, 2, 3, 4, 5) end <- c(3, 4, 5, 7, 2, 4, 6, 7) str <- rep(c("+", "+", "-", "-"), 2) chr <- rep(c("chr1", "chr2"), each = 4) rd <- RangedData(IRanges(start=sta, end=end), strand=str, space=chr) reduce(rd) ####works fine rd2 <- RangedData(IRanges(start=sta, end=end), space=chr) reduce(rd2) ####Error in endoapply(x[, by], FUN) : 'FUN' did not produce an endomorphism rd3 <- RangedData(IRanges(start=sta, end=end), fakename=rep("hello",8),space=chr) reduce(rd3) ####works fine thanks very much, Janet Young

Janet, I'll patch IRanges to fix this. For now you can use the workaround: RangedData(reduce(ranges(rd2))) Patrick Janet Young wrote: > Hi Patrick, > > I second Robert's thanks - reduce on RangedData is really useful. > > I have an additional suggestion (you might already be on the case with this > one). I was trying to reduce a RangedData object that didn't have any > strand/score/name, and kept getting an error > (Error in endoapply(x[, by], FUN) : 'FUN' did not produce an endomorphism). > I got around that by just adding a fake name (or strand or whatever) that is > identical for all objects. > > It would be even nicer if reduce could handle bare bones RangedData objects > without needing this workaround. > > Here is some code to show you what I mean, following your example: > > suppressMessages(library(IRanges)) > sta <- c(1, 2, 5, 6, 2, 3, 4, 5) > end <- c(3, 4, 5, 7, 2, 4, 6, 7) > str <- rep(c("+", "+", "-", "-"), 2) > chr <- rep(c("chr1", "chr2"), each = 4) > rd <- RangedData(IRanges(start=sta, end=end), strand=str, space=chr) > reduce(rd) ####works fine > > rd2 <- RangedData(IRanges(start=sta, end=end), space=chr) > reduce(rd2) > ####Error in endoapply(x[, by], FUN) : 'FUN' did not produce an endomorphism > > rd3 <- RangedData(IRanges(start=sta, end=end), fakename=rep("hello",8),space=chr) > reduce(rd3) ####works fine > > thanks very much, > > Janet Young > > _______________________________________________ > Bioconductor mailing list > Bioconductor at stat.math.ethz.ch > https://stat.ethz.ch/mailman/listinfo/bioconductor > Search the archives: http://news.gmane.org/gmane.science.biology.informatics.conductor >