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?
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
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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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