Found what was wrong with my code changed: inFile <- file('gwas_data_chr10.gen') to: inFile <- file('gwas_data_chr10.gen','r') Dunno why its important but it is :P -- View this message in context: http://r.789695.n4.nabble.com/Read-file-line-by-line-tp3602349p3602399.html Sent from the R help mailing list archive at Nabble.com.