Steve, Converting to a matrix resulted in a much larger increase in speed compared with treating the columns as list. Here are the comparison results for a 100 by 100 data frame. id <- 4:ncol(mydata) system.time(for (i in id) { mydata[[i]] <- ifelse(mydata[[i]] > 0, 1, mydata[[i]])} ) user system elapsed 0.034 0.000 0.037 system.time(for (i in id) { mydata[,i] <- ifelse(mydata[,i] > 0, 1, mydata[,i])} ) user system elapsed 0.038 0.003 0.042 system.time({m <- as.matrix(mydata[, -(id)]) m[m > 0] <- 1 ans <- cbind(mydata[,1:4], as.data.frame(m))}) user system elapsed 0.006 0.000 0.009 Many thanks for your great suggestions! Best regards, Julie On 12/28/11 3:10 PM, "Julie Zhu" <julie.zhu at="" umassmed.edu=""> wrote: > Thanks, Steve, > > Matrix is definitely faster. I will try with list to see if it makes it > faster. > > Best regards, > > Julie > > > On 12/28/11 3:06 PM, "Steve Lianoglou" <mailinglist.honeypot at="" gmail.com=""> > wrote: > >> Hi, >> >> On Wed, Dec 28, 2011 at 3:01 PM, Zhu, Lihua (Julie) >> <julie.zhu at="" umassmed.edu=""> wrote: >>> Hi, >>> >>> I have a data frame consisting of 5000 columns and 16000 rows. I would like >>> to convert all values x in column 4 to 5000 to 1 if x >0. The following code >>> works but it is very slow. Are there more efficient ways to modify large >>> number of entries in a data frame? Many thanks for your kind help! >>> >>> id <- 4:ncol(mydata) >>> for (i in id) {mydata[mydata[,i]>0,i]=1} >> >> You might have better results if you treat the columns of the >> data.frame as a list, so something like: >> >> for (i in 4:ncol(mydata)) { >> mydata[[i]] <- ifelse(mydata[[i]] > 0, 1, mydata[[i]]) >> } >> >> >> ## Or, what if you convert to a matrix? >> m <- as.matrix(mydata[, -(1:4)]) >> m[m > 0] <- 1 >> ans <- cbind(mydata[,1:4], as.data.frame(m)) >> >> >> Are any of those better? >> >> -steve > > _______________________________________________ > Bioconductor mailing list > Bioconductor at r-project.org > https://stat.ethz.ch/mailman/listinfo/bioconductor > Search the archives: > http://news.gmane.org/gmane.science.biology.informatics.conductor