[BioC] annotate() and genbank and XML

[Andrew Yee]

Hi, I'm looking for some guidance in terms of parsing the XML output
from a genbank query.

result <- genbank('NM_000610', disp='data', type='uid')

I'm trying to figure out how to use the XML package in order to parse
out the "sig_peptide" field from the XML output from the genbank
query.

Any pointers or suggestions would be appreciated, as I'm new to XML.

Thanks,
Andrew



> sessionInfo()
R version 2.13.0 (2011-04-13)
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] XML_3.2-0             annotate_1.29.4       AnnotationDbi_1.13.21
[4] Biobase_2.11.10

loaded via a namespace (and not attached):
[1] DBI_0.2-5     RSQLite_0.9-4 tools_2.13.0  xtable_1.5-6