So you would expect that the DNAStringSet is converted to a character vector? DNAStringSet (technically XStringSet) then just needs an as.vector method that delegates to as.character.
Michael On Wed, Jun 15, 2011 at 12:37 PM, Janet Young <[email protected]> wrote: > Hi there, > > I'm trying to as as.data.frame on a GRanges object. On regular GRanges > objects it works fine but I have some objects that contain a DNAStringSet in > the values column, which isn't built in to the as.data.frame method. Is it > possible to add the ability to coerce the DNAStringSet too, please? > > Here's some code that demonstrates the issue: > > ################ > library(GenomicRanges) > library(Biostrings) > > gr1 <- > GRanges(seqnames=rep("chr1",3),ranges=IRanges(start=c(1,101,201),width=50),strand=c("+","-","+"), > genenames=c("seq1","seq2","seq3") ) > > as.data.frame(gr1) > # works > > gr2 <- gr1 > values(gr2)[,"myseqs"] <- DNAStringSet(c ("AACGTG", "ACGGTGGTGTT", > "GAGGCTG")) > > as.data.frame(gr2) > # Error in as.data.frame.default(y, optional = TRUE, ...) : > # cannot coerce class 'structure("DNAStringSet", package = "Biostrings")' > into a data.frame > ################ > > and here's sessionInfo() output: > > R version 2.13.0 (2011-04-13) > Platform: i386-apple-darwin9.8.0/i386 (32-bit) > > locale: > [1] en_US.UTF-8/en_US.UTF-8/C/C/en_US.UTF-8/en_US.UTF-8 > > attached base packages: > [1] stats graphics grDevices utils datasets methods base > > other attached packages: > [1] Biostrings_2.20.1 GenomicRanges_1.4.6 IRanges_1.10.4 > > ################ > > > You might wonder why I'm storing sequences in the GRanges values - in my > real data they're sequencing reads that have mapped back to that region, but > I'm still curious to maintain the sequence itself (for the moment) because > it's not always identical to the underlying genomic sequence of that region > (investigating mapping issues). > > (and my desire to use as.data.frame relates to a suggestion from Herve to > let me workaround some issues with the identical function) > > thanks, > > Janet > > _______________________________________________ > Bioc-sig-sequencing mailing list > [email protected] > https://stat.ethz.ch/mailman/listinfo/bioc-sig-sequencing > [[alternative HTML version deleted]] _______________________________________________ Bioc-sig-sequencing mailing list [email protected] https://stat.ethz.ch/mailman/listinfo/bioc-sig-sequencing
