[R] Read file line by line

[Joel]

Hi

I got a file that looks like this: (i have shorten it alot the real file is
over 200k rows long)

chr10 rs7909677 101955 A G 0 1 0 1 0 0...
chr10 rs2436025 238506 C G 1 0 0 1 0 0...
chr10 rs11253562 148946 C T 0 1 0 0 1 ...
chr10 rs1105116 230788 G T 0 0 1 0 0 1...
chr10 rs4881551 149076 A G 0 1 0 0 1 0 0 1...

What I want it to go trough the file and get the highest value in the third
column so to say.
And because the file is so big I don't want to read it all into the memory
so reading in chunks and then traverse it line by line and get the biggest
number.

What I've experiment with is something like this

inFile <- file('gwas_data_chr10.gen')
output <- 0
while(length(input <- readLines(inFile, n=1000)) > 0){
 for (i in seq_along(input)){
  temp<-as.numeric(strsplit(input[i], " +")[[1]][3])
  if(output<temp){
   output<-temp
  }
 }
}
close(inFile)

The problem is that it seems to get stuck on an infinity loop of the 1000
first rows of the file, it dossent continue with the next 1000 from the
first loop so to say.

Can someone see the error in my code or dose anyone have an other solution
to the problem?

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