I'm interested to work with .gen file generated from IMPUTE2 imputation tool. In particular I need probabilities per SNP. I use snpStats' function:
test_impute<-read.impute("genotyped_snps_chr22.impute", rownames = NULL, nsnp = NULL, snpcol = 2)
But the output I get is snpMatrix, which I fail to unpack and access. Is there a way I can see first 10 rows and column from this matrix?
show(test_impute) class(test_impute) summary(test_impute) attributes(test_impute) This prints all SNP ids on screen names(test_impute)
None of these help.
Is there a better way that could allow me to access these probabilities for my downstream analysis?
I'm looking at gtx package's
read.snpdata.impute function - but this is awfully slow. I've 13K snps in the input file.
snpStats_1.28.0 Matrix_1.2-14 gtx_0.0.8 survival_2.42-3
R version 3.4.2 (2017-09-28) Platform: x86_64-pc-linux-gnu (64-bit)