[BioC] PFAM annotation from HyperG

Dario Greco dario.greco at helsinki.fi
Tue Jun 12 13:02:12 CEST 2007

dear list,
i am running HyperG test in Category package for finding over-representation 
of KEGG pathways and PFAM terms.
i would like to annotate the results from the PFAM analysis. is there anything 
similar to getPathNames() also for the PFAM terms?

i have installed the package PFAM but it does something strange:

> pfamAC2DE()
[1] "14-3-3 protein"

it has only one pfam-id. am i missing something?

here is my sessionInfo:

> sessionInfo()
R version 2.5.0 (2007-04-23)


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

other attached packages:
    PFAM  RSQLite      DBI
"1.16.1"  "0.5-4"  "0.2-3"

thanks in advance for your help!



Dario Greco

Institute of Biotechnology - University of Helsinki
Building Cultivator II
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FIN-00014       Finland

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