unusual behavior when concatenating DNAStringSets
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Andrew Yee ▴ 350
@andrew-yee-2667
Last seen 7.3 years ago
Hi, I've posted the same question to the bio-sig-sequencing list ( https://stat.ethz.ch/pipermail/bioc-sig- sequencing/2010-September/001564.html) two days ago, but also interested to see if the main Bioconductor group has any input as follows: I encountered some unusual behavior when concatenating multiple DNAStringSet objects as follows: library('Biostrings') x <- DNAStringSet('ATA') y <- DNAStringSet('GCG') z <- DNAStringSet('AGA') foo <- rep(list(x,y,z),1) # I was exploring to see if the length of the list made a difference (it doesn't) do.call(c, foo) # creates a DNAStringSet names(foo) <- c('x', 'y', 'z') do.call(c, foo) # creates a DNAStringSet names(foo) <- c('a', 'b', 'c') do.call(c, foo) # creates a list instead, not a DNAStringSet It seems that in the last case, a list is created rather than a DNAStringSet. It seems that the operation in sensitive to the names() of the list. Or is there an alternative means of concatenating multiple DNAStringSets? Thanks, Andrew > sessionInfo() R version 2.11.1 Patched (2010-09-04 r52880) Platform: x86_64-unknown-linux-gnu (64-bit) locale: [1] LC_CTYPE=en_US.UTF-8 LC_NUMERIC=C [3] LC_TIME=en_US.UTF-8 LC_COLLATE=en_US.UTF-8 [5] LC_MONETARY=C LC_MESSAGES=en_US.UTF-8 [7] LC_PAPER=en_US.UTF-8 LC_NAME=C [9] LC_ADDRESS=C LC_TELEPHONE=C [11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C attached base packages: [1] stats graphics grDevices utils datasets methods base other attached packages: [1] Biostrings_2.16.9 IRanges_1.6.17 loaded via a namespace (and not attached): [1] Biobase_2.8.0 [[alternative HTML version deleted]]
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@martin-morgan-1513
Last seen 1 day ago
United States
On 09/24/2010 05:51 AM, Andrew Yee wrote: > Hi, I've posted the same question to the bio-sig-sequencing list ( > https://stat.ethz.ch/pipermail/bioc-sig- sequencing/2010-September/001564.html) > two days ago, but also interested to see if the main Bioconductor group has > any input as follows: > > I encountered some unusual behavior when concatenating multiple > DNAStringSet objects as follows: > > library('Biostrings') > > x <- DNAStringSet('ATA') > y <- DNAStringSet('GCG') > z <- DNAStringSet('AGA') > > foo <- rep(list(x,y,z),1) # I was exploring to see if the length of the list > made a difference (it doesn't) > do.call(c, foo) # creates a DNAStringSet > > names(foo) <- c('x', 'y', 'z') > do.call(c, foo) # creates a DNAStringSet > > names(foo) <- c('a', 'b', 'c') > do.call(c, foo) # creates a list instead, not a DNAStringSet Hi Andrew -- I have partially answered your original post. Martin > > It seems that in the last case, a list is created rather than a > DNAStringSet. It seems that the operation in sensitive to the names() > of the list. Or is there an alternative means of concatenating > multiple DNAStringSets? > > Thanks, > Andrew > > >> sessionInfo() > R version 2.11.1 Patched (2010-09-04 r52880) > Platform: x86_64-unknown-linux-gnu (64-bit) > > locale: > [1] LC_CTYPE=en_US.UTF-8 LC_NUMERIC=C > [3] LC_TIME=en_US.UTF-8 LC_COLLATE=en_US.UTF-8 > [5] LC_MONETARY=C LC_MESSAGES=en_US.UTF-8 > [7] LC_PAPER=en_US.UTF-8 LC_NAME=C > [9] LC_ADDRESS=C LC_TELEPHONE=C > [11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C > > attached base packages: > [1] stats graphics grDevices utils datasets methods base > > other attached packages: > [1] Biostrings_2.16.9 IRanges_1.6.17 > > loaded via a namespace (and not attached): > [1] Biobase_2.8.0 > > [[alternative HTML version deleted]] > > _______________________________________________ > Bioconductor mailing list > Bioconductor at stat.math.ethz.ch > https://stat.ethz.ch/mailman/listinfo/bioconductor > Search the archives: http://news.gmane.org/gmane.science.biology.informatics.conductor
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