pyRAD.loci object with a subset of paired sample names that differ
only by a suffix (defined here as
this function will return a table summarizing the overlap pattern
overlap.report(dat, repPattern = "_re", origPattern = "_h")
an object of class
suffix for the first half of each pair
suffix for the second half of each pair
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.
a matrix with pairs of individuals as rows and overlap statistics as columns
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.
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