[BioC] RangedData Element Metadata

Dario Strbenac D.Strbenac at garvan.org.au
Fri Mar 30 08:00:23 CEST 2012


I have two bigWig files read in by using a function from rtracklayer. I'm trying to do a simple subtraction of the coverage values. I use

diff <- values(bws[[2]])[,1] - values(bws[[1]])[,1]

I'd like to assign this to one of the bws and write it out again, but I can't because values <- requires a SplitDataFrameList.

I had a look at the function definition : SplitDataFrameList(..., compress = TRUE, cbindArgs = FALSE)
on page 9 of the reference manual and then I tried to use it, by converting diff to a data.frame first, but seemingly there is no constructor :

> SplitDataFrameList(tmp)
Error: could not find function "SplitDataFrameList"

How can I put the diff values back into one of the RangedData objects ?

> sessionInfo()
R version 2.14.2 (2012-02-29)
Platform: x86_64-unknown-linux-gnu (64-bit)

 [1] LC_CTYPE=en_AU.UTF-8       LC_NUMERIC=C              
 [3] LC_TIME=en_AU.UTF-8        LC_COLLATE=en_AU.UTF-8    
 [7] LC_PAPER=C                 LC_NAME=C                 
 [9] LC_ADDRESS=C               LC_TELEPHONE=C            

attached base packages:
[1] parallel  stats     graphics  grDevices utils     datasets  methods  
[8] base     

other attached packages:
[1] rtracklayer_1.14.4 RCurl_1.91-1       bitops_1.0-4.1    

loaded via a namespace (and not attached):
[1] Biobase_2.11.10     Biostrings_2.22.0   BSgenome_1.19.6    
[4] GenomicRanges_1.6.7 IRanges_1.12.6      tools_2.14.2       
[7] XML_3.4-0           zlibbioc_1.0.1

Dario Strbenac
Research Assistant
Cancer Epigenetics
Garvan Institute of Medical Research
Darlinghurst NSW 2010

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