Converts a StAMPP formated allele frequency data frame generated from the stamppConvert function to a genlight object for use in other packages
Arguments
- geno
a data frame containing allele frequency data generated from stamppConvert
- pop
logical. True if population IDs are present in the StAMPP genotype data, False if population IDs are absent.
Value
A object of class genlight which contains genotype data, individual IDs, population IDs (if present) and ploidy levels
Details
StAMPP only exports to genlight objects as they are able to handle mixed ploidy datasets unlike genpop and genloci objects. The genlight object allows the intergration between StAMPP and other common R packages such as ADEGENET
Examples
# import genotype data and convert to allele frequecies
data(potato.mini, package="StAMPP")
potato.freq <- stamppConvert(potato.mini, "r")
# Convert the StAMPP formatted allele frequency data frame to a genlight object
potato.genlight <- stampp2genlight(potato.freq, TRUE)