8.10 Merging genotype and phenotype data

To perform a GWAS, we need to combine genotype and phenotype information for the same individuals. This means merging these two data for our SNP of interest, which we do with the merge function:

# merge genotype and phenotype info for test SNP
gwas_data <- merge(test_snp_gt, phenotypes,
                   by.x = "Indiv", by.y = "IID")

head(gwas_data)

##   Indiv ChromKey    POS gt_GT gt_GT_alleles dosage  FID GS451_IC50
## 1  1001        1 558185   0/0           A/A      0 1001   5.594256
## 2  1002        1 558185   0/0           A/A      0 1002   8.525633
## 3  1003        1 558185   0/0           A/A      0 1003  12.736739
## 4  1004        1 558185   0/1           A/G      1 1004  12.175201
## 5  1005        1 558185   0/0           A/A      0 1005   9.936742
## 6  1006        1 558185   0/1           A/G      1 1006   9.163483