[Bioc-sig-seq] unusual behavior when concatenating DNAStringSets

[Andrew Yee]

I encountered some unusual behavior when concatenating multiple
DNAStringSet objects as follows:

library('Biostrings')

x <- DNAStringSet('ATA')
y <- DNAStringSet('GCG')
z <- DNAStringSet('AGA')

foo <- rep(list(x,y,z),1)
do.call(c, foo) # creates a DNAStringSet

names(foo) <- c('x', 'y', 'z')
do.call(c, foo) # creates a DNAStringSet

names(foo) <- c('a', 'b', 'c')
do.call(c, foo) # creates a list instead, not a DNAStringSet

It seems that in the last case, a list is created rather than a
DNAStringSet.  It seems that the operation in sensitive to the names()
of the list.  Or is there an alternative means of concatenating
multiple DNAStringSets?

Thanks,
Andrew


> sessionInfo()
R version 2.11.1 Patched (2010-09-04 r52880)
Platform: x86_64-unknown-linux-gnu (64-bit)

locale:
 [1] LC_CTYPE=en_US.UTF-8       LC_NUMERIC=C
 [3] LC_TIME=en_US.UTF-8        LC_COLLATE=en_US.UTF-8
 [5] LC_MONETARY=C              LC_MESSAGES=en_US.UTF-8
 [7] LC_PAPER=en_US.UTF-8       LC_NAME=C
 [9] LC_ADDRESS=C               LC_TELEPHONE=C
[11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C

attached base packages:
[1] stats     graphics  grDevices utils     datasets  methods   base

other attached packages:
[1] Biostrings_2.16.9 IRanges_1.6.17

loaded via a namespace (and not attached):
[1] Biobase_2.8.0