Hi,
I found out, that XStringViews/Views subsetting operator does not reduce
element metadata as I would expect. See the following example. It is
reproducible in both stable (2.11) and development (2.12) versions of
Bioconductor.
------------------------------------------------
library(Biostrings)
x <- Views(DNAString("GAA"), 1:2, 2:3)
elementMetadata(x) <- DataFrame(score=3:4)
y <- x[1]
elementMetadata(y) <- elementMetadata(y)
------------------------------------------------
The example fails with following error message:
------------------------------------------------
Error in `elementMetadata<-`(`*tmp*`, value = <S4 object of class
"DataFrame">) :
the number of rows in elementMetadata 'value' (if non-NULL) must match
the length of 'x'
------------------------------------------------
Output of sessionInfo()
------------------------------------------------
R version 2.15.2 (2012-10-26)
Platform: x86_64-pc-linux-gnu (64-bit)
locale:
[1] LC_CTYPE=cs_CZ.UTF-8 LC_NUMERIC=C
[3] LC_TIME=cs_CZ.UTF-8 LC_COLLATE=cs_CZ.UTF-8
[5] LC_MONETARY=cs_CZ.UTF-8 LC_MESSAGES=cs_CZ.UTF-8
[7] LC_PAPER=C LC_NAME=C
[9] LC_ADDRESS=C LC_TELEPHONE=C
[11] LC_MEASUREMENT=cs_CZ.UTF-8 LC_IDENTIFICATION=C
attached base packages:
[1] stats graphics grDevices utils datasets methods base
other attached packages:
[1] Biostrings_2.26.3 IRanges_1.16.5 BiocGenerics_0.4.0
loaded via a namespace (and not attached):
[1] parallel_2.15.2 stats4_2.15.2
------------------------------------------------
As I do not orient well in XStringViews inheritance structure, I can't
even guess, where a significance change was made. I only know that in Bioc
2.8.4 (R 2.13.1) is this example fully functional.
Please take a look at this issue and if it's not a bug, but a feature,
please be patient and explain.
Thanks a lot
Jirka
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