This function calculates Nei's genetic distance (Nei 1972) between populations or individuals
a data frame containing allele frequency data generated from stamppConvert, or a genlight object containing genotype data, individual IDs, population IDs and ploidy levels
logical. True if genetic distance should be calculated between populations, false if it should be calculated between individual
A object of class matrix which contains the genetic distance between each population or individual
Luke Pembleton <luke.pembleton at agriculture.vic.gov.au>
Nei M (1972) Genetic Distance between Populations. The American Naturalist 106, 283-292.
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# import genotype data and convert to allele frequecies data(potato.mini, package="StAMPP") potato.freq <- stamppConvert(potato.mini, "r") # Calculate genetic distance between individuals potato.D.ind <- stamppNeisD(potato.freq, FALSE) # Calculate genetic distance between populations potato.D.pop <- stamppNeisD(potato.freq, TRUE)
Loading required package: pegas Loading required package: ape Loading required package: adegenet Loading required package: ade4 Registered S3 method overwritten by 'spdep': method from plot.mst ape /// adegenet 2.1.3 is loaded //////////// > overview: '?adegenet' > tutorials/doc/questions: 'adegenetWeb()' > bug reports/feature requests: adegenetIssues() Registered S3 method overwritten by 'pegas': method from print.amova ade4 Attaching package: ‘pegas’ The following object is masked from ‘package:ade4’: amova The following object is masked from ‘package:ape’: mst
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