aggregate by factor

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?

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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