[BioC] Getting GO ids for genenames in plasmodium falciparum

Ipsi [guest] guest at bioconductor.org
Tue Oct 8 10:09:53 CEST 2013

I have a list of genenames - plasmodium falciparum gotten from the plasmodb website. 

I am trying to get the associated GO:IDs in order to bin the genes into housekeeping versus non-housekeeping genes.
And also in terms of functional and process.

I have installed the org.Pf.plasmo.db using biocLite.

I have tried to use this example:

 x <- org.Pf.plasmoGO
    # Get the ORF identifiers that are mapped to a GO ID
    mapped_genes <- mappedkeys(x)
    # Convert to a list
    xx <- as.list(x[mapped_genes])
    if(length(xx) > 0) {
        # Try the first one
        got <- xx[[1]]           

It doesnt provide an opportunity to create a column and enter my own gene names. It appears to be a premapped set of genenames. As a result I decided to use the example to get all mappings in the list xx 

Unfortunately, I am unable to iterate through the list to generate it in a dataframe to meaningfully divide up the data. 

Secondly is there a way to actually query a database directly via R to get the associated GO:ID where the input would be a genename. 

Sorry to sound confused. I am pretty new to R and bioconductor.

 -- output of sessionInfo(): 

R version 3.0.1 (2013-05-16)
Platform: x86_64-w64-mingw32/x64 (64-bit)

[1] LC_COLLATE=English_United States.1252  LC_CTYPE=English_United States.1252    LC_MONETARY=English_United States.1252
[4] LC_NUMERIC=C                           LC_TIME=English_United States.1252    

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

other attached packages:
 [1] org.Pf.plasmo.db_2.9.0 BiocInstaller_1.10.3   GO.db_2.9.0            hgu95av2.db_2.9.0      org.Hs.eg.db_2.9.0    
 [6] RSQLite_0.11.4         DBI_0.2-7              AnnotationDbi_1.22.6   Biobase_2.20.1         BiocGenerics_0.6.0    

loaded via a namespace (and not attached):
 [1] digest_0.6.3       grid_3.0.1         gtable_0.1.2       IRanges_1.18.4     plyr_1.8           proto_0.3-10      
 [7] RColorBrewer_1.0-5 reshape2_1.2.2     stats4_3.0.1       stringr_0.6.2      tools_3.0.1       

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