On Fri, Aug 10, 2012 at 11:07 AM, Janet Young <jayoung@fhcrc.org> wrote: > Hi, > > Thanks, Michael. > > I ended up with a different and less elegant solution: > geneInfo <- import.bed(myBedFileThreeGenes, asRangedData=FALSE) > geneLengths <- sapply( values(geneInfo)$blocks, function(x) { > sum(width(x)) } ) > names(geneLengths) <- values(geneInfo)$name > > Interestingly, test$blocks works but values(test)$blocks gives > NULL. That seems a little non-intuitive, but I kinda see why. (my first > thought was along the lines of your solution, but I got caught by > values(test)$blocks not working - I think the difference between RangedData > and GRanges is confusing me once again). > > Yea, it's confusing. The values() function on RangedData returns a DataFrameList that is indexed by e.g. chromosome. You could do a values(test)[,"blocks"] I think. > Janet > > > On Aug 10, 2012, at 6:16 AM, Michael Lawrence wrote: > > Hi Janet, > > Sorry, the blocks() function has fallen into disrepair. I will check-in a > fix for it soon. > > To solve your problem, there is no need to use blocks(). Simply get the > "blocks" column out, which is a RangesList, and sum up its widths. > > Like: > > sum(width(test$blocks)) > > Michael > > On Wed, Aug 8, 2012 at 7:25 PM, Janet Young <jayoung@fhcrc.org> wrote: > >> Hi there, >> >> A quick question - I'm a little confused about how to use the "blocks" >> function of rtracklayer - can you help? I think perhaps I'm just not >> understanding the help page right and not understanding what should be >> possible and what should not. I'm looking at ?blocks (and ?import.bed). >> From those pages, it seems like the following code should work, but I get >> errors. I'm missing something, I think.... >> >> I think i'll be able to find another more convoluted way to do what I >> want to do, which is to get the total transcript size from a bed file that >> contains block information, but it seems like this simpler way should work >> - any suggestions? >> >> Thanks, >> >> Janet Young >> >> ---------- >> >> library(rtracklayer) >> >> ### read in a bed file: (this example is from the help page ?import.bed >> and has some block information) >> >> test_path <- system.file("tests", package = "rtracklayer") >> test_bed <- file.path(test_path, "test.bed") >> >> test <- import(test_bed) >> class(test) >> #[1] "UCSCData" >> #attr(,"package") >> #[1] "rtracklayer" >> >> test2 <- as(test, "RangedData") >> class(test2) >> #[1] "RangedData" >> #attr(,"package") >> #[1] "IRanges" >> >> blocks(test2) >> #Error in blocks(as(x, "GenomicRanges")) : >> # error in evaluating the argument 'x' in selecting a method for >> function 'blocks': Error in as(x, "GenomicRanges") : >> # no method or default for coercing "RangedData" to "GenomicRanges" >> >> blocks(asBED(test2)) >> #Error in blocks(asBED(test2)) : >> # error in evaluating the argument 'x' in selecting a method for >> function 'blocks': Error in function (classes, fdef, mtable) : >> # unable to find an inherited method for function "asBED", for signature >> "RangedData" >> >> >> sessionInfo() >> >> R version 2.15.1 (2012-06-22) >> Platform: x86_64-apple-darwin9.8.0/x86_64 (64-bit) >> >> locale: >> [1] en_US.UTF-8/en_US.UTF-8/en_US.UTF-8/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_1.16.3 GenomicRanges_1.8.11 IRanges_1.14.4 >> BiocGenerics_0.2.0 >> >> loaded via a namespace (and not attached): >> [1] Biostrings_2.24.1 bitops_1.0-4.1 BSgenome_1.24.0 RCurl_1.91-1 >> Rsamtools_1.8.6 stats4_2.15.1 tools_2.15.1 >> [8] XML_3.9-4 zlibbioc_1.2.0 >> >> _______________________________________________ >> Bioconductor mailing list >> Bioconductor@r-project.org >> https://stat.ethz.ch/mailman/listinfo/bioconductor >> Search the archives: >> http://news.gmane.org/gmane.science.biology.informatics.conductor >> > > > [[alternative HTML version deleted]]