I am working with rehh package of R.
I have to create an object of class haplohh from the function data2haplohh:
test<-data2haplohh(hap_file="test.hap", map_file="test.map.inp", haplotype.in.columns=TRUE)
Map file seems OK: 1054416 SNPs declared for chromosome 1
Haplotype are in columns with no header
Error in scan(hap_file, what = "character", quiet = TRUE) :
too many items
So the *.hap file has 1054416 lines and 5008 columns(approx 10 GB size), *.map.inp file has 1054416 lines and 5 columns(15 MB size). My systems working RAM memory is 64 GB and 8TB is the storage space
I have an option of chopping up the files but, in this case It would create errors in my calculation. So I need to load the input files as a whole.
Any suggestions would be appreciated. Thanks
