geno_call: Genotype calls

In jendelman/polyBreedR: Genomics-assisted breeding for polyploids (and diploids)

Genotype calls

Description

Genotype calls based on a normal mixture model

Usage

geno_call(
  data,
  filename,
  model.ploidy = 4L,
  sample.ploidy = 4L,
  min.posterior = 0,
  transform = TRUE
)

Arguments

data	matrix (markers x id) of input values for the normal mixture model
filename	CSV filename with the model parameters
model.ploidy	2 or 4 (default)
sample.ploidy	2 or 4 (default)
min.posterior	minimum posterior probability (default 0) for genotype call
transform	TRUE (default) or FALSE whether to apply arcsin square root transformation

Details

The first column of the CSV input file should be the SNP ID, followed by columns for the normal distribution means, standard deviations, and mixture probabilities. Genotype calls are based on the maximum a posteriori (MAP) method. If the posterior probability of the MAP genotype is less than min.posterior, then NA is returned for that sample. By default, an arcsin square root transformation is applied to the input values to match the approach used by R package fitPoly. To use a tetraploid mixture model for diploid samples, set sample.ploidy = 2 and model.ploidy = 4.

Value

matrix of allele dosages (0,1,2,..ploidy) with dimensions markers x individuals

jendelman/polyBreedR documentation built on Jan. 5, 2025, 12:13 a.m.