2011/6/15 Hervé Pagès <hpa...@fhcrc.org>
> Hi Michael, Janet,
>
> I just added an "as.vector" method for XStringSet objects to
> Biostrings 2.21.6:
>
> > library(Biostrings)
> > x <- DNAStringSet(c("aaatg", "gt"))
> > as.vector(x)
> [1] "AAATG" "GT"
>
> But that doesn't solve Janet's problem:
>
> > df <- DataFrame(id=c("ID1", "ID2"), seqs=x)
> > df
> DataFrame with 2 rows and 2 columns
> id seqs
> <character> <DNAStringSet>
> 1 ID1 AAATG
> 2 ID2 GT
> > as.data.frame(df)
>
> Error in as.data.frame.default(y, optional = TRUE, ...) :
> cannot coerce class 'structure("DNAStringSet", package = "Biostrings")'
> into a data.frame
>
> Michael?
>
>
Well, sorry for that. I just added a coercion from Vector to data.frame
through as.vector, so this works. But someone might add a coercion from List
to data.frame that would treat the elements as columns. Would this make
sense? AtomicList to data.frame does something even stranger: it creates a
two column data frame with the unlisted values and names/indices rep'd out
as a factor. Actually, that's kind of cool, since usually one does not have
a list with equal element lengths, but it's somewhat unintuitive. But why
does it apply only to AtomicList? Anyway, given the special correspondence
between a XStringSet and a character vector, we could always add an
as.data.frame method for XStringSet, just to make sure stuff behaves as
expected.
> Thanks,
> H.
>
>
> > sessionInfo()
> R version 2.14.0 Under development (unstable) (2011-05-30 r56024)
> Platform: x86_64-unknown-linux-gnu (64-bit)
>
> locale:
> [1] LC_CTYPE=en_CA.UTF-8 LC_NUMERIC=C
> [3] LC_TIME=en_CA.UTF-8 LC_COLLATE=en_CA.UTF-8
> [5] LC_MONETARY=en_CA.UTF-8 LC_MESSAGES=en_CA.UTF-8
> [7] LC_PAPER=C LC_NAME=C
> [9] LC_ADDRESS=C LC_TELEPHONE=C
> [11] LC_MEASUREMENT=en_CA.UTF-8 LC_IDENTIFICATION=C
>
>
> attached base packages:
> [1] stats graphics grDevices utils datasets methods base
>
> other attached packages:
> [1] Biostrings_2.21.6 IRanges_1.11.10
>
>
>
> On 11-06-15 12:49 PM, Janet Young wrote:
>
>> yes - as.character seems a good choice, I think
>>
>> thanks,
>>
>> Janet
>>
>> On Jun 15, 2011, at 12:46 PM, Michael Lawrence wrote:
>>
>> 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<jayo...@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
>>>
>>> _______________________________________________
>>> Bioc-sig-sequencing mailing list
>>> Bioc-sig-sequencing@r-project.org
>>> https://stat.ethz.ch/mailman/listinfo/bioc-sig-sequencing
>>>
>>>
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>>
>
>
> --
> Hervé Pagès
>
> Program in Computational Biology
> Division of Public Health Sciences
> Fred Hutchinson Cancer Research Center
> 1100 Fairview Ave. N, M1-B514
> P.O. Box 19024
> Seattle, WA 98109-1024
>
> E-mail: hpa...@fhcrc.org
> Phone: (206) 667-5791
> Fax: (206) 667-1319
>
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