On Thu, Nov 4, 2010 at 7:58 AM, Michael Dondrup <michael.dondrup@uni.no>wrote: > Hi, > > I have done a little more testing on the values()<- function and I can only > warn from using it, at least when > there are multiple spaces in the RangedData object. You will have no means > of getting the names back in the right order! > > Even if it wouldn't delete the ranges names, it will shuffle the data, and > I don't see a use-case where this function > could be used in a sensible way. The problem is the order in which the the > data is kept, e.g. i read in some data into a data.frame, > then made a RangedData from it. Then assigning more value columns found in > the data.frame. But the data in the Ranged data object > are no longer in the original order but in the order of the RangedData > sorted by spaces. > I don't see how the function is useless. You simply have to sort the data by chromosome. Or you might generate a DataFrame from the ranges in your RangedData, which then will be in the correct order. A lot of times, data is already sorted by chromosome. The sorting performed by RangedData is a well known weakness, but in practice I encounter it rarely. > > So how are you supposed to get the order right in the DataFrame before > using values()<-? > - it's not possible.... > Why is it not possible? All RangedData does is sort by chromosome. There are definitely specific scenarios where the chromosome is unknown for the data. But in general, I don't see the problem. > Therefore I opt for that either the function is removed, or > that a matching on the row.names of DataFrame is made, and if there is a > difference or no row.names an error is thrown, or that the > data is added in the order of the ranges of the rangedData (that should be > preserving the original order). > If this matching is not made, I see no way of guessing the right order for > the DataFrame. > > I think I would leave it to the user to do this sort of matching. > Some example code to illustrate what I mean: > > > > rd = RangedData(ranges= IRanges(start=1:10, width=1, > names=letters[1:10]), space=sample(1:2, 10, re=T)) > > rn = rownames(rd) # save the names in the right order > > values(rd) = DataFrame(data=letters[1:10], row.names=letters[1:10]) > > rd # it's broken, but you dont see it > In the devel version, this should throw an error. > >row.names(rd) = rn # now, everything is broken, but at least you can see > it: > > rd > > > > > > On Nov 3, 2010, at 9:51 PM, Michael Lawrence wrote: > > > > > > > On Wed, Nov 3, 2010 at 9:06 AM, Michael Dondrup <michael.dondrup@uni.no> > wrote: > > Hi, > > > > I remember having posted something like this earlier. > > > > calling values on a RangedData object deletes the ranges names, if the > DataFrame doesn't have names, is > > that intentional? > > > > > rd = RangedData(ranges=IRanges(start=1:2, width=1, names=c("A","B")), > space=1) > > > rownames(rd) > > [1] "A" "B" > > > values(rd) = DataFrame(somedata=1:2) > > > rownames(rd) > > NULL > > > > > > Definitely a bug, because it yields an invalid object, where the ranges > have names but not the data. The question is how to rectify the names. > You're expecting that if the DataFrame has NULL names, for it to take the > names of the RangedData. That makes sense to me. If the rownames on the > DataFrame were not NULL and different from the RangedData, what should > happen? I'm thinking that should throw an error; that's how ranges<- has > always behaved. > > > > Anyway, I checked in a fix to the devel version. Thanks for reporting > this. > > > > Michael > > > > I can work around this by setting them again: > > > > values(rd) = DataFrame(somedata=1:2, row.names=c("A","B")) > > but that's still a glitch... > > > > Michael > > R version 2.12.0 (2010-10-15) > > Platform: x86_64-apple-darwin9.8.0/x86_64 (64-bit) > > > > locale: > > [1] en_US.UTF-8/en_US.UTF-8/C/C/en_US.UTF-8/en_US.UTF-8 > > > > attached base packages: > > [1] stats graphics grDevices utils datasets methods base > > > > other attached packages: > > [1] rtracklayer_1.10.0 RCurl_1.4-3 bitops_1.0-4.1 > IRanges_1.8.0 > > > > _______________________________________________ > > Bioconductor mailing list > > Bioconductor@stat.math.ethz.ch > > https://stat.ethz.ch/mailman/listinfo/bioconductor > > Search the archives: > http://news.gmane.org/gmane.science.biology.informatics.conductor > > > > [[alternative HTML version deleted]]