solarius (version 0.2.3)

phenodata: dat50 data set adapted from FFBSKAT R package

Description

A mixture of unrelated and related individuals were 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.

Usage

phenodata
kin
genodata
genocovdata
snpdata

source

http://mga.bionet.nsc.ru/soft/FFBSKAT/

Details

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.

Examples

data(dat50)

str(phenodata)
plotKinship2(2*kin)
str(genodata)

genodata[1:5, 1:5]
str(genocovdata)

genocovdata[1:5, 1:5]

# compare with the genotypes
genodata[1:5, 1:5]
str(snpdata)

head(snpdata)