GWAS() function error rrBLUP package for GWAS

Question

[giulia.trauzzi]

Hi everyone,

I have been trying to run the function GWAS() in the R package rrBLUP to test for association between my SNPs and 1 phenotypic trait. The function runs and it returns the following error

Error in GWAS(pheno2, geno, min.MAF = 0.05, plot = FALSE) : 
The following lines have phenotypes but no genotypes:

followed by the list of lines at which this occurs.

I have checked for matching IDs between the two input files: phenotypes and genotypes and they are all matching. I also checked for NAs, and replaced them in both files with imputed values.

This is my code to run the function

GWAS <- GWAS(pheno2, geno, min.MAF = 0.05, plot=FALSE)

Has anyone had the same issue/experience?

Thanks
Giulia