Fake a "bigSNP"
snp_fake(n, m)Number of individuals.
Number of SNPs.
A new temporary bigSNP object representing n individuals
and m SNPs. The genotype Filebacked Big Matrix is initialized
with missing values.
(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
#>
#> $map
#> chromosome marker.ID genetic.dist physical.pos allele1 allele2
#> 1 1 snp_1 0 1000 T C
#> 2 1 snp_2 0 2000 C T
#> 3 1 snp_3 0 3000 T C
#> 4 1 snp_4 0 4000 C T
#> 5 1 snp_5 0 5000 T C
#> 6 1 snp_6 0 6000 C T
#> 7 1 snp_7 0 7000 T C
#> 8 1 snp_8 0 8000 C T
#> 9 1 snp_9 0 9000 C T
#> 10 1 snp_10 0 10000 T C
#> 11 1 snp_11 0 11000 T C
#> 12 1 snp_12 0 12000 C T
#>
#> attr(,"class")
#> [1] "bigSNP"
# The genotype Filebackeg Big Matrix is initialized with missing values
G <- test$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 2 1 0 NA NA 0 2 1 0 NA
#> [2,] 1 1 0 2 NA 0 1 1 2 1 1 NA
#> [3,] 2 2 0 1 NA 0 2 2 1 0 1 NA
#> [4,] 2 1 1 2 0 1 2 1 2 1 1 2
#> [5,] 2 NA 2 0 NA 2 1 1 1 2 0 NA