read.Structure {assignPOP}R Documentation

Read Structure format file


This function allows you to import a STRUCTURE format file into R. The first row should be locus name (either with or withour column names for sample ID and population label); the first column should be sample ID; the second column should be population label; the rest are genotype. Use "-9" for missing alleles.


read.Structure(x, ploidy = 2)



STRUCTURE file or path to the file. The filename extension (e.g., .txt) should be included.


An integer of 1, 2, 3, or 4, to indicate haploid, diploid, triploid, or tetraploid data. Default is 2 (diploid).


This function returns a list comprising three elements. 1. YOU_NAME_IT$DataMatrix: A matrix of genetic data with a population name label ($popNameVector) in the last column. 2. YOU_NAME_IT$SampleID: A vector of sample ID. 3. YOU_NAME_IT$LocusName: A vector of locus name.


Pritchard, J.K., Stephens, M. and Donnelly, P., 2000. Inference of population structure using multilocus genotype data. Genetics, 155(2), pp.945-959.


# infile <- read.Structure("Your_Structure_File.txt")

[Package assignPOP version 1.2.4 Index]