adegenet (version 2.0.0)

genlight-class: Formal class "genlight"

Description

The class genlight is a formal (S4) class for storing a genotypes 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 be reduced more than 50 times. However, genlight can be used for any level of ploidy, and still remain an efficient storage mode.

A genlight object can be constructed from vectors of integers giving the number of the second allele for each locus and each individual (see 'Objects of the class genlight' below).

genlight stores multiple genotypes. Each genotype is stored as a SNPbin object.

Details

=== On the subsetting using [ === The function [ accepts the following extra arguments: [object Object],[object Object],[object Object]

See Also

Related class: - SNPbin, for storing individual genotypes of binary SNPs - genind, for storing other types of genetic markers.

Examples

## TOY EXAMPLE ##
## create and convert data
dat <- list(toto=c(1,1,0,0), titi=c(NA,1,1,0), tata=c(NA,0,3, NA))
x <- new("genlight", dat)
x

## examine the content of the object
names(x)
x@gen
x@gen[[1]]@snp # bit-level coding for first individual

## conversions
as.list(x)
as.matrix(x)

## round trips - must return TRUE
identical(x, new("genlight", as.list(x))) # list
identical(x, new("genlight", as.matrix(x))) # matrix
identical(x, new("genlight", as.data.frame(x))) # data.frame

## test subsetting
x[c(1,3)] # keep individuals 1 and 3
as.list(x[c(1,3)])
x[c(1,3), 1:2] # keep individuals 1 and 3, loci 1 and 2
as.list(x[c(1,3), 1:2])
x[c(TRUE,FALSE), c(TRUE,TRUE,FALSE,FALSE)] # same, using logicals
as.list(x[c(TRUE,FALSE), c(TRUE,TRUE,FALSE,FALSE)])


## REAL-SIZE EXAMPLE ##
## 50 genotypes of 1,000,000 SNPs
dat <- lapply(1:50, function(i) sample(c(0,1,NA), 1e6, prob=c(.5, .49, .01), replace=TRUE))
names(dat) <- paste("indiv", 1:length(dat))
print(object.size(dat), unit="aut") # size of the original data

x <- new("genlight", dat) # conversion
x
print(object.size(x), unit="au") # size of the genlight object
object.size(dat)/object.size(x) # conversion efficiency



#### cbind, rbind ####
a <- new("genlight", list(toto=rep(1,10), tata=rep(c(0,1), each=5), titi=c(NA, rep(1,9)) ))

ara <- rbind(a,a)
ara
as.matrix(ara)

aca <- cbind(a,a)
aca
as.matrix(aca)


#### subsetting @other ####
x <- new("genlight", list(a=1,b=0,c=1), other=list(1:3, letters,data.frame(2:4)))
x
other(x)
x[2:3]
other(x[2:3])
other(x[2:3, treatOther=FALSE])


#### seppop ####
pop(x) # no population info
pop(x) <- c("pop1","pop1", "pop2") # set population memberships
pop(x)
seppop(x)