I very new to R and having a little trouble with CdfEnvAffy, I am going
thought the

Here are my steps
>fasta.filename <- system.file("/Users/vmd/Dropbox/dna/toxodb/",
"TgondiiME49Genomic_ToxoDB-6.0.fasta", package = "altcdfenvs")
> con <- file(fasta.filename, open = "r")
Warning message:
In file(fasta.filename, open = "r") :
  file("") only supports open = "w+" and open = "w+b": using the former

#### Not sure what to do about this error so I just removed, <open = "r">,
this seems to be ok

>con <- file(fasta.filename)

#### This is where I am really stuck

> while (!is.null(fasta.seq$header)) {print(fasta.seq) fasta.seq <-
read.FASTA.entry(con)}
Error: unexpected symbol in "while (!is.null(fasta.seq$header))
{print(fasta.seq) fasta.seq"

#### So I tried this and it is better but still not right
> while (!is.null(fasta.seq$header)) {print(fasta.seq) (fasta.seq <-
read.FASTA.entry(con))}
FASTA sequence:
   >gnl|UG|Hs#S1730546 membrane-spanning 4-domains, subfamily A ...
   AACCCATTTCAACTGCCTATTCAGAGCATGCAGTAAGAGGAAATCCACCAAGTCTCAATA ...
Error: attempt to apply non-function


So I am not sure how to get this to work.
Thanks
Vincent


> sessionInfo()
R version 2.10.1 (2009-12-14)
x86_64-apple-darwin9.8.0

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] altcdfenvs_2.8.0    hypergraph_1.18.0   graph_1.24.4
 makecdfenv_1.24.0   affyio_1.14.0
 [6] matchprobes_1.18.0  Biostrings_2.14.12  IRanges_1.4.16
 AnnotationDbi_1.8.2 affy_1.24.2
[11] Biobase_2.6.1

loaded via a namespace (and not attached):
[1] DBI_0.2-5            preprocessCore_1.8.0 RSQLite_0.8-4
 tools_2.10.1



  *Vincent Davis
720-301-3003 *
vincent@vincentdavis.net
 my blog <http://vincentdavis.net> |
LinkedIn<http://www.linkedin.com/in/vincentdavis>

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