On Sat, Oct 23, 2010 at 7:03 PM, Alison Waller <alison.wal...@embl.de> wrote:
> Thanks!
>
> I tried reading the help for aggregate and can't figure out which form of
> the formula I am using, and therefore the syntax.
>
> I'm getting the below error.
>
>> aggregate(counts ~ ind, merge(stack(CAT2COG), df, by = 1), sum)
> Error in as.data.frame.default(x) :
> cannot coerce class "formula" into a data.frame
>> aggregate(counts ~ Cats, merge(stack(CAT2COG), df, by = 1), sum)
> Error in as.data.frame.default(x) :
> cannot coerce class "formula" into a data.frame
>> Cats
> [1] A B C D E
> Levels: A B C D E
>> aggregate(counts ~ COGs, merge(stack(CAT2COG), df, by = 1), sum)
> Error in as.data.frame.default(x) :
> cannot coerce class "formula" into a data.frame
> On 24-Oct-10, at 12:50 AM, Gabor Grothendieck wrote:
>
>>> aggregate(counts ~ ind, merge(stack(CAT2COG), df, by = 1), sum)
>
>
Maybe you have too old a version of R?
I am using this version:
> R.version.string
[1] "R version 2.11.1 Patched (2010-05-31 r52167)"
Here is a self contained example using the objects you posted:
> CAT2COG<-list(A="COG1",B=c("COG1","COG2"),C=c("COG1","COG3"),D=c("COG2","COG4"))
> df<-data.frame(COGs=c("COG1","COG2","COG3","COG4"),counts=c(10,20,30,40))
> aggregate(counts ~ ind, merge(stack(CAT2COG), df, by = 1), sum)
ind counts
1 A 10
2 B 30
3 C 40
4 D 60
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