Accessors {adegenet}R Documentation

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.

Usage




Value

A genind or genpop object.

Author(s)

Thibaut Jombart jombart@biomserv.univ-lyon1.fr

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

[Package adegenet version 1.1-0 Index]