Question: Importing huge data into GenABEL
0
gravatar for Paula Sanchez
4.4 years ago by
Spain
Paula Sanchez0 wrote:

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.

gwas snp R genome • 2.0k views
ADD COMMENTlink modified 3.9 years ago by Biostar ♦♦ 20 • written 4.4 years ago by Paula Sanchez0

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

ADD REPLYlink written 4.3 years ago by komal.rathi3.5k

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

ADD REPLYlink written 3.9 years ago by Jean-Karim Heriche21k

What version of R?  What version of GenABEL?

ADD REPLYlink written 3.9 years ago by Sean Davis25k

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 !!

ADD REPLYlink written 2.7 years ago by always_learning1000
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