This function calculates the centers for standardization based on the estimated bias from the `updog` package. It identifies genotype dosage clusters and determines whether markers should be retained or removed based on the number of clusters.
updog_centers(multidog_obj, threshold.n.clusters = 2, rm.mks)A named list where each element corresponds to a marker and contains: - `rm`: An integer flag indicating whether the marker is retained (`0`) or removed (`1`). - `centers_theta`: A numeric vector of cluster centers (sorted in descending order). - `MarkerName`: The name of the marker. - `n.clusters`: The number of clusters identified for the marker.
An object of class `multidog` (from the `updog` package), containing information about SNPs, ploidy, sequencing error rates, and bias.
An integer specifying the minimum number of dosage clusters (heterozygous classes) required for a marker to be retained for standardization. Default is `2`.
A logical vector indicating which markers should be removed. The names of the vector correspond to the marker names.
The function uses the `xi_fun` to calculate the cluster centers for each marker based on the ploidy, sequencing error rate, and bias. Markers with fewer clusters than the specified threshold are flagged for removal.