Fake a "bigSNP"

snp_fake(n, m)

Arguments

n

Number of individuals.

m

Number of SNPs.

Value

A new temporary bigSNP object representing n individuals and m SNPs. The genotype Filebacked Big Matrix is initialized with missing values.

Examples

(test <- snp_fake(5, 12))
#> $genotypes #> A Filebacked Big Matrix of type 'code 256' with 5 rows and 12 columns. #> #> $fam #> family.ID sample.ID paternal.ID maternal.ID sex affection #> 1 fam_1 ind_1 0 0 0 -9 #> 2 fam_2 ind_2 0 0 0 -9 #> 3 fam_3 ind_3 0 0 0 -9 #> 4 fam_4 ind_4 0 0 0 -9 #> 5 fam_5 ind_5 0 0 0 -9 #> #> $map #> chromosome marker.ID genetic.dist physical.pos allele1 allele2 #> 1 1 snp_1 0 1000 C T #> 2 1 snp_2 0 2000 T C #> 3 1 snp_3 0 3000 C T #> 4 1 snp_4 0 4000 T C #> 5 1 snp_5 0 5000 C T #> 6 1 snp_6 0 6000 C T #> 7 1 snp_7 0 7000 C T #> 8 1 snp_8 0 8000 C T #> 9 1 snp_9 0 9000 C T #> 10 1 snp_10 0 10000 C T #> 11 1 snp_11 0 11000 T C #> 12 1 snp_12 0 12000 T C #> #> attr(,"class") #> [1] "bigSNP"
# The genotype Filebackeg Big Matrix is initialized with missing values G <- test$genotypes G[]
#> [,1] [,2] [,3] [,4] [,5] [,6] [,7] [,8] [,9] [,10] [,11] [,12] #> [1,] NA NA NA NA NA NA NA NA NA NA NA NA #> [2,] NA NA NA NA NA NA NA NA NA NA NA NA #> [3,] NA NA NA NA NA NA NA NA NA NA NA NA #> [4,] NA NA NA NA NA NA NA NA NA NA NA NA #> [5,] NA NA NA NA NA NA NA NA NA NA NA NA
# Modify the genotype `big.matrix` G[] <- sample(as.raw(0:3), size = length(G), replace = TRUE) G[]
#> [,1] [,2] [,3] [,4] [,5] [,6] [,7] [,8] [,9] [,10] [,11] [,12] #> [1,] 0 NA 1 NA 1 2 2 2 0 NA 1 0 #> [2,] 2 0 2 NA 1 2 NA 0 NA 2 0 0 #> [3,] 1 2 2 1 1 NA 1 NA 0 0 NA 0 #> [4,] 0 NA 1 1 1 1 NA 0 2 0 NA 2 #> [5,] NA 1 1 0 0 2 2 NA 1 NA NA 1