[BioC] BioStrings - BStringViews Object

Mayra Eduardoff mayra.eduardoff at tcri.at
Mon Mar 3 16:32:49 CET 2008

Hi ,

I am now using R version 2.6.0 (2007-10-03)


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

other attached packages:
[1] Biobase_1.16.1   Biostrings_2.6.4 RMySQL_0.6-0     DBI_0.2-4
[5] biomaRt_1.12.2   RCurl_0.8-3

loaded via a namespace (and not attached):
[1] rcompgen_0.1-15 XML_1.93-2

I was wondering whether the writeFASTA() function is not reading in
BStringViews object anymore ? It only seems to work with a list.

[1] "BStringViews"
[1] "Biostrings"

writeFASTA(bsv, "Doc/tables/pta-seq.fasta")
Error in writeFASTA(bsv, "Doc/tables/pta-seq.fasta") :
  invalid type/length (S4/1) in vector allocation

My other question is whether the BStringViews object is only thought
to be used for different views on the same BString ? I kept using it
for different BString-objects to i.e use the function complement(),
but I guess I shoud have sapplied the function to a vector of
DNAStrings or something like that ?



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