When comparing the results of assignClones and GenoType using my own data, the only differences I have seen have been the result of rounding a decimal that was slightly above the threshold in when analyzed in R was rounded down to the threshold when analyzed in GenoType. Note that GenoType requires that distances be integers rather than decimals, so you will have to multiply the distances produced by polysat by a large number and round them to the nearest integer if you wish to export them to GenoType. If a distance matrix from polysat is exported to GenoType, the results will be the same as those from assignClones assuming the same threshold is used.
GENODIVE SAMPLE DATA MATRIX SOFTWARE
Each clone or group is given a number, and the number for each sample indicates the clone or group to which it belongs.ĭetails: This function groups individuals very similarly to the software GenoType (Meirmans and van Tienderen, 2004). Return Values: A numeric vector, named by samples. # assign clones with a threshold of zero or 0.5 # set up a simple matrix with three samples Install.packages("polysat", repo="", dep=T) A number indicating the maximum distance between two individuals that will be placed into the same group.
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