pegas (version 0.1)

summary.loci: Print and Summaries of Loci Objects

Description

These functions print and summarize table of alleles and loci (objects of class "loci".

Usage

## S3 method for class 'loci':
print(x, details = FALSE, ...)
## S3 method for class 'loci':
summary(object, ...)
## S3 method for class 'summary.loci':
print(x, ...)
## S3 method for class 'summary.loci':
plot(x, loci, what = "both", layout = 1, col = c("blue", "red"), ...)

Arguments

x, object

an object of class "loci" or "genind", a data frame, a factor, or a vector.

details

a logical value: if TRUE the data are printed as a data frame; the default is FALSE.

loci

the loci (genes) to be plotted. By default, all loci are plotted

what

the frequencies to be plotted. Three choices are possible: "alleles", "genotypes", and "both" (the default), or any unambiguous abbreviations.

layout

the number of graphs to be plotted simultaneously.

col

the colours used the barplots.

...

further arguments to be passed to or from other methods.

Value

• summary.loci returns a list with the genes as names and each element made a list with two vectors "genotype" and "allele" with the frequencies (numbers) of genotypes and alleles, respectively. The names of these two vectors are the observed genotypes and alleles.

  print and plot methods return NULL.

Details

Genotypes not observed in the data frame are not counted.

See Also

read.loci, getAlleles