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
>>
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>>
>
>
>

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