Make the snp array for genotype data
make_snpsGeno(genotyped)| genotyped | object from variantAnnotation::readVcf |
|---|
snp array encoded as integers
snpsGeno <- make_snpsGeno(snpsGeno_VCF)
snpsGeno[1:5, 1:5]
#> 4463344375_R01C01 4463344375_R01C02 4572348848_R01C02
#> chr1:4712657_G/A 2 2 2
#> chr1:7853370_G/A 2 0 1
#> chr1:8949385_A/C 1 2 1
#> chr1:8974362_G/A 1 0 1
#> chr1:9263851_G/A 1 1 1
#> 4572348855_R01C02 5535549043_R01C01
#> chr1:4712657_G/A 1 0
#> chr1:7853370_G/A 1 1
#> chr1:8949385_A/C 1 1
#> chr1:8974362_G/A 2 0
#> chr1:9263851_G/A 0 1