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 <jayoung@fhcrc.org> 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
>
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>

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