I am trying to import a huge data file into GenABEL, but I am having trouble. I have 15,000 bulls (30 Chromosomes) genotyped with 700,000 SNPs.
My genotype files is coded as:
Name Chr Pos 238570 238632 238757 238591
BT_17218 1 17218 AB AB AB AB
BT_18426 1 18426 AA -- AA AB
BT_20658 1 20658 AB AA AB BB
BT_28296 1 28296 BB AB BB --
BT_31152 1 31152 AB AB BB AB
When I try to convert into GenABEL object I get the following error:
data <- load.gwaa.data(phe = "pheno.txt", gen = "geno.raw", force=T)
marker names loaded...
chromosome data loaded...
map data loaded...
allele coding data loaded...
strand data loaded...
Error in scan(file, what, nmax, sep, dec, quote, skip, nlines, na.strings, :
too many items
What would be the best option for me to convert this data? Thanks in advance.