Description Usage Arguments Value Author(s) Examples
Identify duplicate or very similar genotypes.
1 | dupGenotypes(g, num.shared = 0.8)
|
g |
a gtypes object. |
num.shared |
either number of loci or percentage of loci two individuals must share to be considered duplicate individuals. |
if no duplicates are present, the result is NULL
, otherwise
a data frame with the following columns is returned:
ids.1, ids.2 | sample ids. |
strata.1, strata.2 | sample stratification. |
mismatch.loci | loci where the two samples do not match. |
num.loci.genotyped | number of loci genotyped for both samples. |
num.loci.shared | number of loci shared (all alleles the same) between both samples. |
prop.loci.shared | proportion of loci genotyped for both samples that are shared. |
Eric Archer eric.archer@noaa.gov
1 2 3 4 5 6 7 | data(msats.g)
# identify potential duplicates in Coastal strata
coastal <- msats.g[, , "Coastal"]
coastal.5 <- coastal[getIndNames(coastal)[1:5], , ]
dupes <- dupGenotypes(coastal.5)
dupes
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