I tried your proposition Sarah (I was answering to Berend when you posted
your answer).
Well it seems to work! 
I just had to add afterwords a line to have my NAs again.
I converted values = 0 by NA (numeric() in the function did the contrary for
the calculation):

mydata[mydata==0] <- NA 

At first it was working for such kind of data: NAs just in the middle of my
data
test <-
data.frame(c(1,2,3,4,NA,NA,7,8,9,10),c(11,12,NA,14,15,16,17,NA,19,20))
colnames(test)<- c("data1","data2")

but not for data with NAs at the beginning, in the middle and at the end:

test2 <-
data.frame(c(NA,2,3,4,NA,NA,NA,NA,NA,NA),c(NA,12,13,NA,15,16,17,NA,NA,NA))
colnames(test2)<- c("data3","data4")

But thanks to your proposition, it seems to work in both cases now!
Thanks a lot sarah!

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