A mixture of unrelated and related individuals was originally simulated in FFBSKAT R package to test methods of the variant-collapsing approach. 50 synthetic SNPs were generated for the association study. A custom kinship matrix is used to express the relationships among individuals. This data set is used here to test the ability of SOLAR to work with a custom kinship matrix in both polygenic and association analyses.
(Phenotypes) A data frame
phenodata with 66 rows and 4 variables:
Individual gender (0 - male, 1 - female).
(Kinship) A square matrix
kin with 66 rows and 66 columns.
(Genotypes) A matrix
genodata with 66 rows and 50 columns.
(Genotypes as covariates) A matrix
genocovdata with 66 rows and 50 columns.
(Annotation) A data frame
snpdata with 100 rows and 4 variables:
Position in bp.
The genotypes are coded in the format such as 1/1, 1/2 and 2/2.
In addition to the original data set from FFBSKAT R package, a matrix of covariates was derived from the genotype data according to the additive model.
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