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Structure.jl

PopGenCore.jl/src/io/Structure.jl​

📦 not exported🟪 exported by PopGenCore.jl🔵 exported by PopGen.jl

📦 phase_structure​

phase_structure(datatype::DataType, args...)

Takes a DataType (such as Int8) and a series of integers to return a sorted Tuple of those integers converted to that DataType. i.e. takes a series of alleles and returns a genotype. Returns missing if args are missing. Used internally in PopGen.structure file reader.

Example​

phase_structure(Int8, 1,2,3,4,3,4,6,1)
(1, 1, 2, 3, 3, 4, 4, 6)

phase_structure(Int16, missing, missing)
missing

🟪 structure​

structure(infile::String; kwargs...)

Load a Structure format file into memory as a PopData object.

  • infile::String : path to Structure file

Keyword Arguments​

  • extracols::Integer: how many additional optional columns there are beyond Stucture's POPDATA the reader needs to ignore (default: 0)
    • these include POPFLAG, LOCDATA, or anything else you might have added
  • extrarows::Integer : how many additional optional rows there are beyond the first row of locus names (default: 0)
  • missingval::String : the value used to identify missing values in the data (default: "-9")
  • silent::Bool : whether to print file information during import (default: false)
  • allow_monomorphic::Bool : whether to keep monomorphic loci in the dataset (default: false)
  • faststructure::Bool: whether the file is fastStructure format (default: false)

File must follow this Structure format:​

  • the file is tab or space delimited but not both
  • first row is locus names separated by the delimiter
    • leading/trailing whitespaces are tolerated
    • optional rows allowed after the locus names
  • number of rows per sample = ploidy
    • e.g. if diploid, that sample would have 2 rows
    • multi-column variant not supported
  • first data column is sample name
  • second data column is population ID
    • optional columns allowed after the population ID (2nd) column
  • remaining columns are the genotype for that individual for that locus

Structure file example:​

locus_1 locus_2 locus_3 locus_4 locus_5
walnut_01   1   -9  145 66  0   92
walnut_01   1   -9  -9  64  0   94
walnut_02   1   106 142 68  1   92
walnut_02   1   106 148 64  0   94
walnut_03   2   110 145 -9  0   92
walnut_03   2   110 148 66  1   -9

fastStructure file format:​

  • the file is tab or space delimited but not both
  • no first row of loci names
  • number of rows per sample = ploidy
    • e.g. if diploid, that sample would have 2 rows
  • first data column is sample name
  • second data column is population ID
  • remaining columns are the genotype for that individual for that locus
  • usually, first 6 colums are empty (but not necessary)
  • no extra rows or columns.

fastStructure file example:​

chestnut_01 1   -9  145 66  0   92
chestnut_01 1   -9  -9  64  0   94
chestnut_02 1   106 142 68  1   92
chestnut_02 1   106 148 64  0   94
chestnut_03 2   110 145 -9  0   92
chestnut_03 2   110 148 66  1   -9

Example

walnuts = structure("juglans_nigra.str", extracols = 0, extrarows = 0)
structure(data::PopData; filename::String, faststructure::Bool, delim::String)

Write a PopData object to a Stucture format file

  • data: the PopData object you wish to convert to a Structure file

keyword arguments​

  • filename: a String of the output filename
  • delim : a String of either "tab" or "space" indicating the delimiter (default: "tab")
  • faststructure: true/false of whether the output should be formatted for fastStructure (default: false)

Example

cats = @nancycats;
fewer_cats = omit(cats, name = samplenames(cats)[1:10]);
structure(fewer_cats, filename = "filtered_nancycats.str", faststructure = true)