Should be fixed in 1.17.9. If you're using release, might be easiest to
just get rid of that last column.

Michael

On Wed, Jun 6, 2012 at 10:46 AM, Michael Lawrence <michafla@gene.com> wrote:

>
>
> On Wed, Jun 6, 2012 at 10:37 AM, swaraj basu <projectbasu@gmail.com>wrote:
>
>> Hello Everybody,
>>
>> I was using the rtracklayer package to upload CAGE tag bed files as
>> genomic
>> ranges object.  I used the commands
>>
>> library(rtracklayer)
>> tmp<-import("filename.bed", asRangedData=FALSE)
>> And they were working fine.
>> My BED file contains 7 fields in the bed format
>>
>> *chr1    3783    3784    ctss1    0.128643307100390    +    1
>> chr1    3788    3789    ctss2    0.128643307100390    +    1
>> chr1    3798    3799    ctss3    0.128643307100390    +    1
>> chr1    3822    3823    ctss4    0.128643307100390    +    1
>> chr1    3830    3831    ctss5    0.128643307100390    +    1
>> chr1    3843    3844    ctss6    0.128643307100390    +    1
>> chr1    3862    3863    ctss7    0.128643307100390    +    1
>> chr1    6254    6255    ctss8    0.128643307100390    -    1
>> chr1    7219    7220    ctss9    0.128643307100390    +    1
>> chr1    14028    14029    ctss10    0.128643307100390    +    1*
>>
>> Recently I did an update of all the installed bioconductor packages using
>> the commands
>> source("http://bioconductor.org/biocLite.R")
>> biocLite(character(), ask=FALSE)
>>
>> And now when I try to upload the same file I get error
>> tmp <- import("filename.bed", asRangedData=FALSE)
>> Error in .Call2("solve_user_SEW0", start, end, width, PACKAGE = "IRanges")
>> :
>>  solving row 1: range cannot be determined from the supplied arguments
>> (too many NAs)
>>
>> While if I upload another bed file with all 12 fields I am not getting any
>> error message
>> eg
>> *chr1    25630757    25636172    ul45    0    +    0    0    0,0,0    5
>> 1142,2065,91,323,482,    0,1399,4271,4518,4933,
>> chr1    25631826    25634542    ul46    0    -    0    0    0,0,0    1
>> 2716,    0,
>> chr1    25631826    25635826    ul47    0    -    0    0    0,0,0    1
>> 4000,    0,
>> chr1    28599188    28604017    ul48    0    -    0    0    0,0,0    4
>> 1086,116,336,221,    0,1199,1425,4608,
>> chr1    40911858    40912963    ul49    0    +    0    0    0,0,0    1
>> 1105,    0,*
>>
>> Is this a change made in the update, or the new version of
>> *rtracklayer*can only accommodate complete bed files. Can someone
>> please help.
>>
>>
> Hi Swaraj,
>
> You're splitting the BED file at a place that does not make a lot of sense
> to me, i.e., between the thickStart and thickEnd columns. When rtracklayer
> goes to load the thick regions, it can find only the start, not the end,
> and it fails. Anyway, this is a bug in rtracklayer and I will go ahead and
> make it assume the missing thickEnd is equal to the feature end.
>
> Michael
>
>
>> -Regards
>>
>> --
>> Swaraj Basu
>> PhD Student (Bioinformatics - Functional Genomics)
>> Animal Physiology and Evolution
>> Stazione Zoologica Anton Dohrn
>> Naples
>>
>>        [[alternative HTML version deleted]]
>>
>> _______________________________________________
>> 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]]

