Accessors {adegenet} | R Documentation |
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.
- "obj[nloc=c("L1","L3")]" returns an object keeping only the loci
specified in the loc
argument (using generic names, not true
names; in this example, only the first and the third locus would be
retained)
The argument treatOther
handles the treatment of objects in the
@other
slot (see 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.
Thibaut Jombart jombart@biomserv.univ-lyon1.fr
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$loc.names # or more simply nancycats[loc=c("L2","L7")] obj$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