adegenet (version 1.4-2)

SNPbin-class: Formal class "SNPbin"

Description

The class SNPbin is a formal (S4) class for storing a genotype of binary SNPs in a compact way, using a bit-level coding scheme. This storage is most efficient with haploid data, where the memory taken to represent data can reduced more than 50 times. However, SNPbin can be used for any level of ploidy, and still remain an efficient storage mode.

A SNPbin object can be constructed from a vector of integers giving the number of the second allele for each locus.

SNPbin stores a single genotype. To store multiple genotypes, use the genlight class.

See Also

Related class: - genlight, for storing multiple binary SNP genotypes. - genind, for storing other types of genetic markers.

Examples

#### HAPLOID EXAMPLE ####
## create a genotype of 100,000 SNPs
dat <- sample(c(0,1,NA), 1e5, prob=c(.495, .495, .01), replace=TRUE)
dat[1:10]
x <- new("SNPbin", dat)
x
x[1:10] # subsetting
as.integer(x[1:10])

## try a few accessors
ploidy(x)
nLoc(x)
head(x$snp[[1]]) # internal bit-level coding

## check that conversion is OK
identical(as(x, "integer"),as.integer(dat)) # SHOULD BE TRUE

## compare the size of the objects
print(object.size(dat), unit="auto")
print(object.size(x), unit="auto")
object.size(dat)/object.size(x) # EFFICIENCY OF CONVERSION


#### TETRAPLOID EXAMPLE ####
## create a genotype of 100,000 SNPs
dat <- sample(c(0:4,NA), 1e5, prob=c(rep(.995/5,5), 0.005), replace=TRUE)
x <- new("SNPbin", dat)
identical(as(x, "integer"),as.integer(dat)) # MUST BE TRUE

## compare the size of the objects
print(object.size(dat), unit="auto")
print(object.size(x), unit="auto")
object.size(dat)/object.size(x) # EFFICIENCY OF CONVERSION


#### c, cbind ####
a <- new("SNPbin", c(1,1,1,1,1))
b <- new("SNPbin", c(0,0,0,0,0))
a
b
ab <- c(a,b)
ab
identical(c(a,b),cbind(a,b))
as.integer(ab)