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 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

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 > > _______________________________________________ > Bioconductor mailing list > Bioconductor@r-project.org > https://stat.ethz.ch/mailman/listinfo/bioconductor > Search the archives: > http://news.gmane.org/gmane.science.biology.informatics.conductor > [[alternative HTML version deleted]]