One possible solution would be to use the existing colnames argument.
Currently, that's constrained to the set of built-in BED columns. That
could be changed so that the non-builtin columns are taken as the names for
the extra columns.

That is flexible but seems error-prone. In this particular use case,
supporting BigBed would be better, since it has a formal mechanism for
describing the extra columns and thus those could be handled automatically.
The only reason we have not supported BigBed is that it relies on a fairly
hefty portion of the UCSC library. Trying to keep that dependency to a
minimum.

Michael

On Mon, Feb 6, 2012 at 3:49 PM, Tengfei Yin <yintengfei@gmail.com> wrote:

> Hi dear all,
>
> I have downloaded some bigBed files from
> ENCODE<
> http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeCaltechRnaSeq/wgEncodeCaltechRnaSeqGm12878R2x75Il200JunctionsRep1V3.bigBed
> >for
> splice junction of RNA-seq data, then I use
> bigBedToBed<
> http://hgdownload.cse.ucsc.edu/admin/exe/linux.x86_64/bigBedToBed>script
> from UCSC  to covert it into a bed file, after that, the header
> looks like
>
> chr1 14830 14970 SJ_2530_GG|CC 649 - 122 -1 89
> chr1 15039 15796 SJ_2730_GG|GC 524 - 61 -1 37
> chr1 15948 16607 SJ_4400_GG|CC 416 - 17 -1 17
> chr1 16766 16858 SJ_5141_GG|TC 300 - 7 -1 7
> chr1 17056 17233 SJ_5424_GG|GC 508 - 61 -1 33
> chr1 17365 17602 SJ_5607_TG|GT 370 - 17 -1 12
>
> it's a BED 6+3 format, so when I try to use import() in rtracklayer, it
> treats column 7,8 as thickStart/thickEnd, and prodcue errors due to
> negative width.
>
> Error in .Call2("solve_user_SEW0", start, end, width, PACKAGE = "IRanges")
> :
>  solving row 1: negative widths are not allowed
>
> Of course I could  just cut it before import or call read.table to get the
> data and covert it as GRanges for downstream analysis, I am just wondering,
> since there are some BED-derived format(ENCODE specific format), like 6+3,
> or 12 + 3, 3+3..., is it possible to make a argument in import.bed() that I
> could specifying a pattern like "6+2", or required.column = 6, and dumped
> all extra column into elementMetadata automatically?
>
> if there is already similar features or I just missed something imporant,
> please let me know and correct me.
>
> Thanks a lot.
>
> Tengfei
>
>
>
> --
> Tengfei Yin
> MCDB PhD student
> 1620 Howe Hall, 2274,
> Iowa State University
> Ames, IA,50011-2274
>
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>
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