On 30 Jan 2010, at 4:20 PM, David Winsemius wrote:
>
> On Jan 30, 2010, at 4:09 PM, david hilton shanabrook wrote:
>
>> I have a data frame with two columns, a factor and a numeric. I want to
>> create data frame with the factor, its frequency and the median of the
>> numeric column
>>> head(motifList)
>> events score
>> 1 aeijm -0.25000000
>> 2 begjm -0.25000000
>> 3 afgjm -0.25000000
>> 4 afhjm -0.25000000
>> 5 aeijm -0.25000000
>> 6 aehjm 0.08333333
>>
>> To get the frequency table of events:
>>
>>> motifTable <- as.data.frame(table(motifList$events))
>>> head(motifTable)
>> Var1 Freq
>> 1 aeijm 110
>> 2 begjm 46
>> 3 afgjm 337
>> 4 afhjm 102
>> 5 aehjm 190
>> 6 adijm 18
>>>
>>
>> Now get the score column back in.
>>
>>> motifTable2 <- merge(motifList, motifTable, by="events")
>>> head(motifTable2)
>> events percent freq
>> 1 adgjm 0.00000000 111
>> 2 adgjm NA 111
>> 3 adgjm 0.13333333 111
>> 4 adgjm 0.06666667 111
>> 5 adgjm -0.16666667 111
>> 6 adgjm NA 111
>>>
>>
>> Then lastly to aggregate on the events column getting the median of the score
>>> motifTable3 <- aggregate.data.frame(motifTable2,
>>> by=list(motifTable2$events), FUN=median, na.rm=TRUE)
>> Error in median.default(X[[1L]], ...) : need numeric data
>>
>> Which gives the error as events are a factor. Can someone enlighten me to a
>> more obvious approach?
>
> I don't think grouping on a factor is the source of your error. You have NA's
> in your data and median will choke on those unless you specify na.rm=TRUE.
>
> --
I thought the na.rm=TRUE in the aggregate function would do this (see above).
I also tried it with
> medianRmNa <- function(data) {
return(median(data, na.rm=TRUE))}
> motifTable3 <- aggregate.data.frame(motifTable2, by=list(motifTable2$events),
> FUN=medianRmNa)
Error in median.default(data, na.rm = TRUE) : need numeric data
same error.
I did leave a line out of the above script,
names(motifTable) <- c("events", "freq")
which helps explain why the merge works
dhs
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