get.parentage: A function to extract the paternity and maternity information...

In jonesor/rcolony: Tools for implementation and visualisation of Colony2 and its outputs

Description

This function extracts the paternity and maternity information from a colony object that was created using get.colony.data. The output is a dataframe with 3 columns. (1) mums, (2) dads, (3) frequency. The output can either be derived from pairwise-likelihood or the full-likelihood method (if available).

Usage

get.parentage(colony.object, pairwise = FALSE)

Arguments

colony.object	A list created by get.colony.data
pairwise	Should the parentage information be derived from the pairwise likelihood estimates (TRUE), of from the full likelihood methods (FALSE). See Wang et al. for details.

Value

A data frame with 3 columns. (1) mums, (2) dads, (3) frequency.

Author(s)

Owen R. Jones

References

Wang, J. (2004) Sibship reconstruction from genetic data with typing errors. Genetics 166: 1963-1979.

See Also

get.colony.data

Examples

data(testdata)
parents<-get.parentage(testdata)
head(parents)

jonesor/rcolony documentation built on May 8, 2019, 11:18 p.m.