Thanks a lot for the interest :)

My loop is the following 
counter = 0
 for (i in 1:nrow(y))
 {


 for (j in 1:ncol(y))
 {
 if (y[i,j]=="Func_0005634") {
         counter = counter + 1 }
 if(y[i,j]=="Func_0005737"){
         counter = counter + 1 } 
 if(y[i,j]=="Func_0005515"){
        counter = counter + 1 }

}
 if(counter == 3 ){
        cat(y[i,1],  file = "foo.csv",  "\n")
        }
 counter = 0

}

and after read.table("foo.csv")

I get 
  V1
1 45

which is the last result

why does it overwrite? how can I have all the results?

Eager to a reply from you!

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