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

[Dario Strbenac]

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