overlap.report: Generates a report on locus overlap between pairs of samples...

In andrew-hipp/RADami: Phylogenetic Analysis of RADseq Data

Generates a report on locus overlap between pairs of samples named in a structured fashion

Description

Provided a pyRAD.loci object with a subset of paired sample names that differ only by a suffix (defined here as repPattern and origPattern), this function will return a table summarizing the overlap pattern

Usage

overlap.report(dat, repPattern = "_re", origPattern = "_h")

Arguments

dat	an object of class pyRAD.loci or summary.pyRAD.loci, or just the indsMat object from a summary.pyRAD.loci object
repPattern	suffix for the first half of each pair
origPattern	suffix for the second half of each pair

Details

This may not be of use to too many people, but we used it in the article below. In our case, the samples were paired technical replicates, but you could imagine sister species, populations or anything else being the replicates of interest.

Value

a matrix with pairs of individuals as rows and overlap statistics as columns

Author(s)

Andrew Hipp

References

Hipp A.L., Eaton D.A.R., Cavender-Bares J., Fitzek E., Nipper R. & Manos P.S. (Accepted pending revision). A framework phylogeny of the American oak clade based on sequenced RAD data. PLoS ONE.

See Also

help, ~~~

Examples

	data(oak.rads)
	overlap.report(oak.rads)

andrew-hipp/RADami documentation built on Nov. 9, 2023, 5:40 p.m.