solarius 0.3.1

dat50 data set adapted from FFBSKAT R package

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/

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.

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)



'data.frame':	66 obs. of  4 variables:
 $ id   : num  1 2 3 4 5 6 7 8 9 10 ...
 $ sex  : int  0 1 0 0 0 1 0 1 1 0 ...
 $ age  : int  80 77 56 44 75 79 75 82 77 76 ...
 $ trait: num  -1.763 -1.423 -0.805 0.268 -1.334 ...





plotKinship2(2*kin)







str(genodata)



 chr [1:66, 1:50] "1/1" "1/1" "1/1" "1/2" "1/2" "1/1" "1/1" ...
 - attr(*, "dimnames")=List of 2
  ..$ : chr [1:66] "1" "2" "3" "4" ...
  ..$ : chr [1:50] "s1" "s2" "s3" "s4" ...




genodata[1:5, 1:5]



  s1    s2    s3    s4    s5   
1 "1/1" "1/1" "1/1" "1/1" "1/1"
2 "1/1" "1/1" "1/1" "1/2" "1/1"
3 "1/1" "1/1" "1/1" "2/2" "1/1"
4 "1/2" "1/1" "1/1" "1/2" "1/2"
5 "1/2" "1/1" "1/1" "1/1" "1/1"





str(genocovdata)



 int [1:66, 1:50] 0 0 0 1 1 0 0 0 0 0 ...
 - attr(*, "dimnames")=List of 2
  ..$ : chr [1:66] "1" "2" "3" "4" ...
  ..$ : chr [1:50] "s1" "s2" "s3" "s4" ...




genocovdata[1:5, 1:5]



  s1 s2 s3 s4 s5
1  0  0  0  0  0
2  0  0  0  1  0
3  0  0  0  2  0
4  1  0  0  1  1
5  1  0  0  0  0



 
# compare with the genotypes
genodata[1:5, 1:5]



  s1    s2    s3    s4    s5   
1 "1/1" "1/1" "1/1" "1/1" "1/1"
2 "1/1" "1/1" "1/1" "1/2" "1/1"
3 "1/1" "1/1" "1/1" "2/2" "1/1"
4 "1/2" "1/1" "1/1" "1/2" "1/2"
5 "1/2" "1/1" "1/1" "1/1" "1/1"





str(snpdata)



'data.frame':	50 obs. of  4 variables:
 $ name    : chr  "s1" "s2" "s3" "s4" ...
 $ chrom   : int  1 1 1 1 1 1 1 1 1 1 ...
 $ position: num  2105324 2105467 2106094 2108138 2109262 ...
 $ gene    : chr  "gene1" "gene1" "gene1" "gene1" ...




head(snpdata)



   name chrom position  gene
2    s1     1  2105324 gene1
6    s2     1  2105467 gene1
10   s3     1  2106094 gene1
11   s4     1  2108138 gene1
15   s5     1  2109262 gene1
20   s6     1  2110294 gene1