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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