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Do leave-one-out self-assignment of individuals in a reference baseline

Source: R/self_assign.R
self_assign.Rd

Returns a tidy data frame

Usage

self_assign(
  reference,
  gen_start_col,
  preCompiledParams = NULL,
  alle_freq_prior = list(const_scaled = 1)
)

Arguments

reference

a two-column format genetic dataset, with "repunit", "collection", and "indiv" columns, as well as a "sample_type" column that has some "reference" entries

gen_start_col

the first column of genetic data in reference

preCompiledParams

Users should never use this option. It is here only so that this function can be called on a precompiled set of parameters with infer_mixture. Don't use this, unless you are one of the package developers...

alle_freq_prior

a one-element named list specifying the prior to be used when generating Dirichlet parameters for genotype likelihood calculations. Valid methods include "const", "scaled_const", and "empirical". See ?list_diploid_params for method details.

Value

a tibble ...

Examples

ale_sa <- self_assign(alewife, 17)
#> Summary Statistics:
#> 
#> 1070 Individuals in Sample
#> 
#> 11 Loci: Aa046, Aa070, Aa074, Aa081, Aa091, Aa093, Ap010, Ap033, Ap038, Ap058, Ap071
#> 
#> 3 Reporting Units: NNE, SNE, MAT
#> 
#> 21 Collections: EMA, STG, PIS, MYS, MON, TBR, GIL, THA, BRI, CON, QUI, HOU, PEQ, MIA, HUD, DEL, NAN, RAP, CHO, ROA, ALL
#> 
#> 6.31% of allelic data identified as missing