[Bioc-sig-seq] GenomeDataList to data.frame Coercion

[Heidi Dvinge]

> Hello,
>
> I tried out an example in the documentation without success.
>
>> gd <- GenomeData(list(chr1 = IRanges(1, 10), chrX = IRanges(2, 5)),
> + organism = "Mmusculus", provider = "UCSC",
> + providerVersion = "mm9")

I think you alrady have a GenomeDataList here, no?
as(gd, "data.frame")
should work.

>> gdl <- GenomeDataList(list(gd))
>> as(gdl, "data.frame")
> NULL

Again, this looks like a list of a list. Does as(gdl[[1]], "data.frame")
work?

HTH
\Heidi
>>
>> sessionInfo()
> R version 2.12.0 (2010-10-15)
> Platform: x86_64-unknown-linux-gnu (64-bit)
>
> locale:
>  [1] LC_CTYPE=en_AU.UTF-8       LC_NUMERIC=C
>  [3] LC_TIME=en_AU.UTF-8        LC_COLLATE=en_AU.UTF-8
>  [5] LC_MONETARY=C              LC_MESSAGES=en_AU.UTF-8
>  [7] LC_PAPER=en_AU.UTF-8       LC_NAME=C
>  [9] LC_ADDRESS=C               LC_TELEPHONE=C
> [11] LC_MEASUREMENT=en_AU.UTF-8 LC_IDENTIFICATION=C
>
> attached base packages:
> [1] grid      stats     graphics  grDevices utils     datasets  methods
> [8] base
>
> other attached packages:
>  [1] BSgenome_1.18.3     Rsamtools_1.2.3     Biostrings_2.18.2
>  [4] gplots_2.8.0        caTools_1.11        bitops_1.0-4.1
>  [7] gdata_2.8.1         gtools_2.6.2        GenomicRanges_1.2.3
> [10] IRanges_1.8.9
>
> loaded via a namespace (and not attached):
> [1] Biobase_2.10.0 tools_2.12.0
>> gd <- GenomeData(list(chr1 = IRanges(1, 10), chrX = IRanges(2, 5)),
> + organism = "Mmusculus", provider = "UCSC",
> + providerVersion = "mm9")
>> gdl <- GenomeDataList(list(gd))
>> as(gdl, "data.frame")
> NULL
>
> --------------------------------------
> Dario Strbenac
> Research Assistant
> Cancer Epigenetics
> Garvan Institute of Medical Research
> Darlinghurst NSW 2010
> Australia
>
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