How to avoid: read.table truncates numeric values beginning with 0

As said in Ben's answer, colClasses is the easier way to do it. Here is an example:

read.table(text = 'col1 col2
           0012 0001245',
           head=T,
           colClasses=c('character','numeric'))

  col1 col2
1 0012 1245      ## col1 keep 00 but not col2

A reproducible example would be nice, but: use the colClasses argument to read.table() to specify that you want this column to be read as a character variable, not numeric. Or make them back into character variables after reading them in, using sprintf to pad the numbers with leading zeros. (The former is probably easier.)