solarius (version 0.3.0.2)

phenodata: dat50 data set adapted from FFBSKAT R package

Description

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.

Format

(Phenotypes) A data frame phenodata with 66 rows and 4 variables:

id

Individual ID.

sex

Individual gender (0 - male, 1 - female).

age

Age.

trait

Simulated phenotype.

(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:

name

SNP name.

chrom

Chromosome.

position

Position in bp.

gene

Gene.

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)