polyIn: A function for calculating informativeness for the inference of ancestry from loci of any ploidy.

Description

This function will calculate Rosenberg et al's, (2003) In for loci of any ploidy level. The statistic can be calculated across all samples or on a pairwise basis. The function is efficient for a large number of loci.

Usage

polyIn(infile = NULL, pairwise = FALSE, para = FALSE)

Arguments

infile

A character string pointing to an input file containing genotypes in a modified genepop format. Rather that genotypes being coded as either two digit or three digit numbers, polyploid genotypes are coded as AABA, AAAA, ... ABAB etc. for a tetraploid or ABA, AAA, ... ABB etc. for a triploid. The overall structure of the input file should be that of a genepop file.

pairwise

A logical argument specifying whether In should be calculated for pairwise population comparisons. Large number of population samples will result in long computation times.

para

A logical argument specifying whether multiple CPU cores should be used. If para = TRUE, all available system CPUs will be used.

Value

If pairwise = TRUE, a list of pairwise matrices for each locus is returned. These list elements are named as per loci names in infile to allow simple indexing for loci of interest. If pairwise = FALSE and named numeric vector is returned.

References

Rosenberg, N., Li, L., Ward, R., and Pritchard, J., (2003) 'Informativeness of genetic markers for inference of of ancestry.', American Journal of Human Genetics, vol. 73, no. 6 pp. 1402-22.