annotation: how to use "character" for function 'select()'
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Guido Hooiveld ★ 3.2k
@guido-hooiveld-2020
Last seen 1 day ago
Wageningen University, Wageningen, the …

I face a small issue, which likely is easy to solve.....:

I would like to automatically retrieve annotation information for expressionSets, but somehow I don't get it to work...:

Error in (function (classes, fdef, mtable) : unable to find an inherited method for function ‘select’ for signature ‘"character"’

Any suggestions to solve this?

Thanks,

Guido

 

 > library(affyPLM)
> affy.data <- ReadAffy()
>
> x.norm <- rma(affy.data)
Background correcting
Normalizing
Calculating Expression
>
> head(featureNames(x.norm))
[1] "1415670_at"   "1415671_at"   "1415672_at"   "1415673_at"   "1415674_a_at"
[6] "1415675_at"  
>
> annotation(x.norm)
[1] "mouse4302"
>
> require(paste(annotation(x.norm),".db", sep=""), character.only=TRUE)
Loading required package: mouse4302.db
Loading required package: org.Mm.eg.db

>
> paste(annotation(x.norm),".db", sep="")
[1] "mouse4302.db"
>
> anno.result <- select(paste(annotation(x.norm),".db", sep=""),
+ keys=featureNames(x.norm), columns=c("ENTREZID","SYMBOL"), keytype="PROBEID")
Error in (function (classes, fdef, mtable)  :
  unable to find an inherited method for function ‘select’ for signature ‘"character"’
>

 

annotation organismdb • 773 views
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@martin-morgan-1513
Last seen 4 days ago
United States

use select(get(paste0(annotation(x.norm), ".db")), ...) or

pkg <- paste0(annotation(x.norm), ".db")
db <- loadNamespace(pkg)[[pkg]]
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Thanks Martin, working nicely now with get!

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