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Adding sample/locus data

PopData's standard/default format includes information on:

  • sample name
  • sample population name
  • sample ploidy
  • sample genotypes
  • locus name
  • locus physical location (basepairs) [optional]
  • locus genetic position (centiMorgans) [optional]

But, sometimes you might want to add more information to the data structure, so there are the mutating functions sampleinfo! and locusinfo! to do that.

adding sampleinfo​

sampleinfo!(::PopData, metadata::Pair{Symbol, Vector}; categorical::Bool = false)
sampleinfo!(::PopData, metadata::Pair{String, Vector}; categorical::Bool = false)

Add an additional column sample information to PopData metadata. Mutates PopData in place. The new values must be in the same order as the samples in sampleinfo(popdata).

Arguments​

  • metadata : A Pair of :ColumnName => [Values]

Keyword Arguments​

  • categorical : Boolean of whether the metadata being added is categorical aka "factors" (default: false)

Example

cats = @nancycats ;
sampleinfo!(cats, :whiskerlength => rand(metadata(cats).samples))
sampleinfo!(cats, "tailcolor" => rand(["orange", "brown"], metadata(cats).samples), categorical = true)
cats
PopData{Diploid, 9 Microsatellite loci}
  Samples: 237
  Populations: 17
  Other Info: ["whiskerlength", "tailcolor"]

adding locus information​

locusinfo!(::PopData, metadata::Pair{Symbol, Vector}; categorical::Bool = false)
locusinfo!(::PopData, metadata::Pair{String, Vector}; categorical::Bool = false)

Add an additional locus information to PopData metadata. Mutates PopData in place. Metadata must be in the same order as the samples in locusinfo(PopData).

Arguments​

  • metadata : A Pair of :ColumnName => [Values]

Keyword Arguments​

  • categorical : Boolean of whether the metadata being added is categorical aka "factors" (default: false)

Example

cats = @nancycats
locusinfo!(cats, :quality => rand(metadata(cats).loci))
cats
PopData{Diploid, 9 Microsatellite loci}
  Samples: 237
  Populations: 17
  Other Info: ["quality"]