aggregate by factor
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.
David Winsemius, MD Heritage Laboratories West Hartford, CT