adegenet (version 1.2-1)

Accessors: Accessors for adegenet objects

Description

Several accessors for genind or genpop objects. The operator "$" and "$<-" are used to access the slots, being equivalent to "@" and "@<-". The operator "[" can be used to access components of the matrix slot "@tab", returning a genind or genpop object. This syntax is the same as for a matrix; for instance: - "obj[,]" returns "obj" - "obj[1:10,]" returns an object with only the first 10 genotypes (if "obj" is a genind) or the first 10 populations (if "obj" is a genpop) of "obj" - "obj[1:10, 5:10]" returns an object keeping the first 10 entities and the alleles 5 to 10. The argument treatOther handles the treatment of objects in the @other slot (see details).

Value

• A genind or genpop object.

encoding

UTF-8

Details

The "[" operator can treat elements in the @other slot as well. For instance, if obj@other$xy contains spatial coordinates, the obj[1:3,]@other$xy will contain the spatial coordinates of the genotypes (or population) 1,2 and 3. This is handled through the argument treatOther, a logical defaulting to TRUE. If set to FALSE, the @other component is not returned. Note that only matrix-like, vector-like and lists can be proceeded in @other. Other kind of objects will issue a warning an be returned as they are.

Examples

data(nancycats)
nancycats
nancycats$pop

# let's isolate populations 4 and 8
temp <- nancycats@pop=="P04" | nancycats@pop=="P08"
obj <- nancycats[temp,]
obj

truenames(obj)$pop

# let's isolate two markers, fca23 and fca90
nancycats$loc.names

# they correspond to L2 and L7
temp <- nancycats$loc.fac=="L2" | nancycats$loc.fac=="L7"
obj <- nancycats[,temp]
obj

obj$loc.fac 
obj$loc.names

# illustrate how other slot is handled
colonies <- genind2genpop(nancycats)
colonies@other$aChar <- "This will not be proceeded"
colonies123 <- colonies[1:3]
colonies
colonies@other$xy