Approach as I understand it:
- Generate 6 kinship matrices built using all but one excluded chromosome (e.g. mapK_I = CHROM II, III, IV, V, X)
- Calculate BLUPs using each kinship matrix
- Subtract BLUPs from phenotype
- Map by simple correlation
For mapK_I:
cor(Y - Y.BLUP ~ marker)$p.value
For all markers on chromosome I