I have a very large imputation file (363GB in total) so I need to convert to a filevector format with GenABEL. My imputation file is in IMPUTE2 format and looks like so standard .imputed file:
21 rs142159069 45000079 T T 1 0 0 etc etc
In other words, each row is a SNP with columns: chr, rsid, position, alleleA, alleleB, and then probabilities of being AA,AB or BB for each sample. There are 80 million SNPs in this file for 766 samples.
I used the following command in GenABEL to run the command:
data<-impute2databel(gen,pheno,outfile,makeprob = TRUE, old = FALSE, dataOutType = "FLOAT")
I get the following errors (and also if I remove the makeprob = TRUE, old = FALSE, dataOutType = "FLOAT" options)
Options in effect: --infile = c(21, 21, 21, 21, 21, 21, 21, 21, 21, 21) --outfile = c(7, 5, 10, 6, 9, 1, 2, 8, 3, 4) --skiprows = OFF --skipcols = 5 --cnrow = ON, using data from file 'c(5,' --rncol = ON, using data from file 'c(45000079,' --transpose = ON --Rmatrix = OFF --nanString = c(5, Can not open file 'c(21,' for reading ERROR in Rstuff:failed in text2fvf_R Index file not exists: ./tmp528216.fvi Error in (function (cl, name, valueClass) :
Clearly something is wrong with my impute gen file. However, I keep checking it looks normal. Has anyone had this issue before? I tried this on a much smaller file of just 10 SNPs and I also get the same error. Many thanks.