genind2genpop: Conversion from a genind to a genpop object

In adegenet: Exploratory Analysis of Genetic and Genomic Data

Conversion from a genind to a genpop object

Description

The function genind2genpop converts genotypes data (genind) into alleles counts per population (genpop).

Usage

genind2genpop(
  x,
  pop = NULL,
  quiet = FALSE,
  process.other = FALSE,
  other.action = mean
)

Arguments

x	an object of class genind.
pop	a factor giving the population of each genotype in 'x' OR a formula specifying which strata are to be used when converting to a genpop object. If none provided, population factors are sought in x@pop, but if given, the argument prevails on x@pop.
quiet	logical stating whether a conversion message must be printed (TRUE,default) or not (FALSE).
process.other	a logical indicating whether the @other slot should be processed (see details).
other.action	a function to be used when processing the @other slot. By default, 'mean' is used.

Details

=== 'missing' argument ===
The values of the 'missing' argument in genind2genpop have the following effects:
- "NA": if all genotypes of a population for a given allele are missing, count value will be NA

- "0": if all genotypes of a population for a given allele are missing, count value will be 0

- "chi2": if all genotypes of a population for a given allele are missing, count value will be that of a theoretical count in of a Chi-squared test. This is obtained by the product of the margins sums divided by the total number of alleles.

=== processing the @other slot ===
Essentially, genind2genpop is about aggregating data per population. The function can do the same for all numeric items in the @other slot provided they have the same length (for vectors) or the same number of rows (matrix-like objects) as the number of genotypes. When the case is encountered and if process.other is TRUE, then these objects are processed using the function defined in other.action per population. For instance, spatial coordinates of genotypes would be averaged to obtain population coordinates.

Value

A genpop object. The component @other in 'x' is passed to the created genpop object.

Author(s)

Thibaut Jombart [e-mail]

See Also

genind, genpop

Examples

## simple conversion
data(nancycats)
nancycats
catpop <- genind2genpop(nancycats)
catpop
summary(catpop)

## processing the @other slot
data(sim2pop)
sim2pop$other$foo <- letters
sim2pop
dim(sim2pop$other$xy) # matches the number of genotypes
sim2pop$other$foo # does not match the number of genotypes

obj <- genind2genpop(sim2pop, process.other=TRUE)
obj$other # the new xy is the populations' centre

pch <- as.numeric(pop(sim2pop))
col <- pop(sim2pop)
levels(col) <- c("blue","red")
col <- as.character(col)
plot(sim2pop$other$xy, pch=pch, col=col)
text(obj$other$xy, lab=row.names(obj$other$xy), col=c("blue","red"), cex=2, font=2)
## Not run: 
data(microbov)
strata(microbov) <- data.frame(other(microbov))
summary(genind2genpop(microbov)) # Conversion based on population factor
summary(genind2genpop(microbov, ~coun)) # Conversion based on country
summary(genind2genpop(microbov, ~coun/spe)) # Conversion based on country and species


## End(Not run)

adegenet documentation built on Feb. 16, 2023, 6 p.m.