Hi Xin,

Could you please sent me your sessionInfo().

btw: You can try to install the dev-version of ggbio(by running
'useDevel(TRUE)'
in R 2.15 and update ggbio), to see if your problem has been fixed or not.

Thanks a lot.

Tengfei



On Mon, Jul 23, 2012 at 6:35 AM, Xin Yang <xin.yang@cimr.cam.ac.uk> wrote:

> Dear members,
>
> I'm using ggbio to get some coverage plot for bam files and I did:
>
>   autoplot(bamfile, which=genesymbol["IFIH1"],**method = "raw")
>>
>
> reading in as Bamfile
>
> Error in .local(data, ...) : method 'raw' require which argument
>
>
> It seems the "which" argument doesn't work and I checked the
> "genesymbol["IFIH1"]" as follows:
>
>   genesymbol["IFIH1"]
>>
>
> GRanges with 1 range and 2 elementMetadata cols:
>
>         seqnames                 ranges strand |      symbol
>  ensembl_id
>
>            <Rle>               <IRanges>   <Rle>  |<character>
>  <character>
>
>   IFIH1     chr2 [163123590, 163175039]      - |       IFIH1
> ENSG00000115267
>
>   ---
>
>   seqlengths:
>
>                     chr1                 chr10 ...                  chrY
>
>                       NA                    NA ...                    NA
>
>   class(genesymbol["IFIH1"])
>>
>
> [1] "GRanges"
>
> attr(,"package")
>
> [1] "GenomicRanges"
>
>
> Does anyone have a solution?
> Many thanks,
>
> Xin
>
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-- 
Tengfei Yin
MCDB PhD student
1620 Howe Hall, 2274,
Iowa State University
Ames, IA,50011-2274
Homepage: www.tengfei.name

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