genetics: summary.genotype – R documentation

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summary.genotype

Allele and Genotype Frequency from a Genotype or Haplotype Object

Description

summary.genotype creates an object containing allele and genotype frequency from a genotype or haplotype object. print.summary.genotype displays a summary.genotype object.

Usage

## S3 method for class 'genotype'
summary(object, ..., maxsum)
  ## S3 method for class 'summary.genotype'
print(x,...,round=2)

Arguments

`object, x`	an object of class `genotype` or `haplotype` (for `summary.genotype`) or an object of class `summary.genotype` (for `print.summary.genotype`)
`...`	optional parameters. Ignored by `summary.genotype`, passed to `print.matrix` by `print.summary,genotype`.
`maxsum`	specifying any value for the parameter maxsum will cause `summary.genotype` to fall back to `summary.factor`.
`round`	number of digits to use when displaying proportions.

Details

Specifying any value for the parameter maxsum will cause fallback to summary.factor. This is so that the function summary.dataframe will give reasonable output when it contains a genotype column. (Hopefully we can figure out something better to do in this case.)

Value

The returned value of summary.genotype is an object of class summary.genotype which is a list with the following components:

locus

locus information field (if present) from x

`allele.names`	vector of allele names
`allele.freq`	A two column matrix with one row for each allele, plus one row for `NA` values (if present). The first column, `Count`, contains the frequency of the corresponding allele value. The second column, `Proportion`, contains the fraction of alleles with the corresponding allele value. Note each observation contains two alleles, thus the `Count` field sums to twice the number of observations.
`genotype.freq`	A two column matrix with one row for each genotype, plus one row for `NA` values (if present). The first column, `Count`, contains the frequency of the corresponding genotype. The second column, `Proportion`, contains the fraction of genotypes with the corresponding value.

print.summary.genotype silently returns the object x.

Author(s)

Gregory R. Warnes greg@warnes.net

Examples

example.data   <- c("D/D","D/I","D/D","I/I","D/D",
                    "D/D","D/D","D/D","I/I","")
g1  <- genotype(example.data)
g1

summary(g1)

genetics

Population Genetics

v1.3.8.1.3

GPL

Authors

Gregory Warnes, with contributions from Gregor Gorjanc, Friedrich Leisch, and Michael Man.

Initial release

2012-11-26