On Fri, Oct 30, 2009 at 3:38 AM, Christian Ruckert <cruckert@uni-muenster.de
> wrote:

> When trying to import the example .bed track from
> http://genome.ucsc.edu/goldenPath/help/customTrack.html#BED with the
> import function from rtracklayer package I get the following error message:
>
> > tr = import("example.bed")
> Error in scan(file, what, nmax, sep, dec, quote, skip, nlines, na.strings,
>  :
>  line 1 did not have 9 elements
>
>
The UCSC browser supports so-called "browser lines" at the top of a file
which sometimes are a convenient way to pass instructions to the browser
upon upload of a track. These are not part of the track data or the BED
format. So each line starting with 'browser' should be removed.


> > sessionInfo()
> R version 2.10.0 RC (2009-10-18 r50160)
> x86_64-pc-linux-gnu
>
> locale:
> [1] C
>
> attached base packages:
> [1] stats     graphics  grDevices utils     datasets  methods   base
>
> other attached packages:
> [1] rtracklayer_1.6.0 RCurl_1.3-0       bitops_1.0-4.1
>
> loaded via a namespace (and not attached):
> [1] BSgenome_1.14.0   Biobase_2.6.0     Biostrings_2.14.0 IRanges_1.4.0
> [5] XML_2.6-0
>
>
> example.bed:
>
> ##Example 5 from Custom Annotation Tracks User's Guide
> browser position chr7:127471196-127495720
> browser hide all
> track name="ItemRGBDemo" description="Item RGB demonstration" visibility=2
> itemRgb="On"
> chr7    127471196       127472363       Pos1    0       +       127471196
>     127472363       255,0,0
> chr7    127472363       127473530       Pos2    0       +       127472363
>     127473530       255,0,0
> chr7    127473530       127474697       Pos3    0       +       127473530
>     127474697       255,0,0
> chr7    127474697       127475864       Pos4    0       +       127474697
>     127475864       255,0,0
> chr7    127475864       127477031       Neg1    0       -       127475864
>     127477031       0,0,255
> chr7    127477031       127478198       Neg2    0       -       127477031
>     127478198       0,0,255
> chr7    127478198       127479365       Neg3    0       -       127478198
>     127479365       0,0,255
> chr7    127479365       127480532       Pos5    0       +       127479365
>     127480532       255,0,0
> chr7    127480532       127481699       Neg4    0       -       127480532
>     127481699       0,0,255
>
>
> Best regards,
> Christian
>
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