Importing huge data into GenABEL

Question

[Paula Sanchez]

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:

geno[1:5,1:7]
 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)
ids loaded...
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.

[komal.rathi]

Can you try splitting the data by chromosome, read it in, and merge the resulting gwaa-data objects?

[Jean-Karim Heriche]

This may be linked to hitting R's maximum number of rows. See here and here.

[Sean Davis]

What version of R? What version of GenABEL?

[always_learning]

Version: R/R-3.2.2 GenABEL: 1.8.0 Did someone find an answer for this? Total data size is 4000 samples and 6 Millions variants !!