Dear Patrick and Michael, thank you very much for your helpful support on my last two connected issued! It is somehow in the documentation in the examples but I must have overlooked it. I tried it out immediately, and it works fine: > rd = RangedData(IRanges(start=1:4, width=10, names=paste("a",1:4)), space=1:2 ) > rd > rd$a.value = rnorm(4) > rd RangedData with 4 rows and 1 value column across 2 spaces space ranges | a.value <character> <iranges> | <numeric> 1 1 [1, 10] | -0.6765515 2 1 [3, 12] | 1.5406962 3 2 [2, 11] | -1.2599696 4 2 [4, 13] | 0.4971178 But then I had to reboot my computer because by accident tried this on a 100,000 ranges and the value was actually a list, not a vector, and then the re- cycling rule struck me: > rd$a.list = as.list(1:4) first everything seems fine and normal but if you try to print it: > rd RangedData with 4 rows and 1 value column across 2 spaces Error in .Method(..., deparse.level = deparse.level) : number of rows of matrices must match (see arg 2) or try to convert into a data.frame: > as.data.frame(rd) space start end width names a.list.1L a.list.2L a.list.3L a.list.4L 1 1 1 10 10 a 1 1 2 3 4 2 1 3 12 10 a 3 1 2 3 4 3 2 2 11 10 a 2 1 2 3 4 4 2 4 13 10 a 4 1 2 3 4 as I tried this, I R ran into some memory problems. This just as a warning, to make sure you really use a vector here. Maybe something to put in the type checking, or documentation? Anyway, thanks a lot again Michael Am Mar 18, 2010 um 6:55 PM schrieb Patrick Aboyoun: > I have been experimenting with S4 dispatch on ... (optional arguments) and reading the man page for dotMethods > > > help(dotsMethods) > > Long story short, adding support for cbind-ing a vector to an S4 object would probably involve either > > 1) creating an S4 class union of an S4 class (e.g. RangedData) with vector so the existing S4 dispatch would choose the correct method or > 2) creating an S4 default method for cbind that has it own dispatch mechanism for choosing a cbind method. > > I don't find either of these options appealing and second Michael Lawrence's suggestion of using "$<-" or "[[<-" to bind new columns to a RangedData object. > > > a.value <- rnorm(4) > > rd1 <- RangedData(ranges=IRanges(start=runif(4, min=1, max=10E8), width=runif(4, min=1, max=10E5), names=paste("bla",1:4)), space=1:2) > > obj <- cbind(rd1, a.value) > > showMethods("cbind") > Function: cbind (package IRanges) > ...="ANY" > ...="DataFrame" > ...="DataFrameList" > ...="DataTable" > ...="numeric#RangedData" > (inherited from: ...="ANY") > > > df1 <- unlist(values(rd1)) > > class(df1) > [1] "DataFrame" > attr(,"package") > [1] "IRanges" > > cbind(df1, a.value) > df1 a.value > [1,] ? -0.6268173 > [2,] ? 2.540871 > [3,] ? 0.4137926 > [4,] ? -0.897856 > > showMethods("cbind") > Function: cbind (package IRanges) > ...="ANY" > ...="DataFrame" > ...="DataFrame#numeric" > (inherited from: ...="ANY") > ...="DataFrameList" > ...="DataTable" > ...="numeric#RangedData" > (inherited from: ...="ANY") > > > sessionInfo() > R version 2.11.0 Under development (unstable) (2010-03-14 r51276) > i386-apple-darwin9.8.0 > > 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] IRanges_1.5.64 > > > On 3/18/10 10:32 AM, Michael Lawrence wrote: >> On Thu, Mar 18, 2010 at 7:55 AM, Michael Dondrup<michael.dondrup at="" uni.no="">wrote: >> >> >>> Hi, >>> here is another little possible glitch with RangedData and cbind(), >>> actually would like to propose to >>> change or expand the behavior of the cbind function or to add to it's >>> documentation. The use-case is as >>> follows: >>> Assume we have some chromosomal Ranges in a RangedData object. Then we can >>> iteratively compute statistics on >>> these ranges and attach them to the DataFrame holding extra data, e.g. some >>> count data or combine qualitiy scores possibly from multiple conditions. >>> >>> So according to the documentation of the RangedData-class, >>> >>>> The first mode treats the object as a contiguous "data frame" annotated >>>> >>> with range information. >>> >>>> The accessors start, end, and width get the corresponding fields in the >>>> >>> ranges as atomic integer vectors, undoing >>> >>>> the division over the spaces. The [[> and matrix-style [, extraction and >>>> >>> subsetting functions unroll the data in the same way. [[<- does the inverse. >>> I assume I could use cbind(rd, a.value) to attach the statistics to the >>> internal data representation. So would it be possible to >>> make cbind return something more useful, or are there better ways to do it? >>> >>> >>> >>> >> Right now it's just using the cbind method for "ANY", because one does not >> exist for RangedData. To be honest, I've always just used the $<- syntax for >> adding the statistics. This seems like it would work well in your use case, >> as well. >> >> Like: >> >> rd$a.value<- a.value >> >> Michael >> >> >> >> >>> Best >>> Michael >>> >>> >>> Example: >>> >>> >>>> a.value = rnorm(4) >>>> rd1 = RangedData(ranges=IRanges(start=runif(4, min=1, max=10E8), >>>> >>> width=runif(4, min=1, max=10E5), names=paste("bla",1:4)), space=1:2) >>> >>>> rd1 >>>> >>> RangedData with 4 rows and 0 value columns across 2 spaces >>> space ranges | >>> <character> <iranges> | >>> bla 1 1 [773679042, 774010137] | >>> bla 3 1 [194819013, 195136171] | >>> bla 2 2 [183105318, 183509803] | >>> bla 4 2 [107730452, 107823748] | >>> >>> >>>> obj = cbind(rd1, a.value) >>>> >>> And I would intuitively assume the result to look exactly like this: >>> >>> >>>> RangedData(ranges=IRanges(start=runif(4, min=1, max=10E8), width=runif(4, >>>> >>> min=1, max=10E5), names=paste("bla",1:4)), space=1:2, a.value) >>> RangedData with 4 rows and 1 value column across 2 spaces >>> space ranges | a.value >>> <character> <iranges> |<numeric> >>> bla 1 1 [473042533, 473820859] | -1.7956588 >>> bla 3 1 [ 75991383, 76022516] | 0.3588571 >>> bla 2 2 [475385363, 476224756] | 1.4166218 >>> bla 4 2 [532603052, 532902678] | 0.2324424 >>> >>> But what I get is much different: >>> >>> >>>> class(obj) >>>> >>> [1] "matrix" >>> >>>> typeof(obj) >>>> >>> [1] "list" >>> >>> >>>> obj >>>> >>> rd1 a.value >>> [1,] ? 0.3255676 >>> [2,] ? 0.5913471 >>> [3,] ? 0.9317755 >>> [4,] ? -0.8897527 >>> >>> >>>> sessionInfo() >>>> >>> R version 2.10.1 (2009-12-14) >>> x86_64-apple-darwin9.8.0 >>> >>> 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] IRanges_1.4.9 >>> >>> loaded via a namespace (and not attached): >>> [1] tools_2.10.1 >>> >>> _______________________________________________ >>> 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 >>> >>> >> [[alternative HTML version deleted]] >> >> _______________________________________________ >> 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 >> >