On Thu, Mar 29, 2012 at 11:00 PM, Dario Strbenac
<D.Strbenac@garvan.org.au>wrote:

> Hello,
>
> 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 think it's as simple as:

score(bws[[1]]) <- score(bws[[2]]) - score(bws[[1]])

Or: bws[[1]][,1] <- diff
Or: bws[[1]][,"score"] <- diff
Or: bws[[1]]$score <- diff




> 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)
>
> 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=en_AU.UTF-8    LC_MESSAGES=en_AU.UTF-8
>  [7] LC_PAPER=C                 LC_NAME=C
>  [9] LC_ADDRESS=C               LC_TELEPHONE=C
> [11] LC_MEASUREMENT=en_AU.UTF-8 LC_IDENTIFICATION=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
> Australia
>
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