I am using Numeric SNP data for GWAS analysis in GAPIT. I am struggling with what value should I use for missing values in my SNP file. I have tried N or NA and the analysis doesnt work and it gives me an error.
try "-9"
"'NA" or "NaN" should work. If not, please post the error message you received.
Hi,
Its still not working and am getting the following error.
[1] "--------------------- Welcome to GAPIT ----------------------------"
[1] "All packages are loaded already ! GAPIT.Version is 2018.08.18, GAPIT 3.0"
[1] "MLM"
[1] "--------------------Processing traits----------------------------------"
[1] "Phenotype provided!"
[1] "GAPIT.DP in process..."
[1] "Reading file: 1 Fragment: 1"
[1] "Geno_SNP_chr1.txt"
[1] "File end reached for GD!!!"
[1] "File end reached for GI!!!"
Error in array(x, c(length(x), 1L), if (!is.null(names(x))) list(names(x), :
'data' must be of a vector type, was 'NULL'
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