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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]]
got[[1]][["GOID"]]
got[[1]][["Ontology"]]
got[[1]][["Evidence"]]
}
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)
locale:
[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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