This is how I transform several columns of a dataframe, i.e., with count-data into binary coded data (this would apply also for any other conversion..).

count1 <- count2 <- count3 <- count4 <- sample(c(rep(0, 10), 1:10))
some <- LETTERS[1:20]  
thing <- letters[1:20]  
mydf <- data.frame(count1, count2, count3, count4, some, thing)

ids <- grep("count", names(mydf))
myfun <- function(x) {ifelse(x > 0, 1, 0)}
mydf[, ids] <- lapply(mydf[, ids], myfun)

p.s.: Let me know if you know of a slicker way.