plot_locus_perm_cv

This function takes a list of list object from the "locus_perm_cv" function and creates a summary graphic of the accuracy, kappa, sensitivity, and specificity of the models ran. If heterozygous individuals were left in the cross validation scheme, by-class sensitivity and specificity will be displayed; otherwise, displayed parameters will be of the overall model.

Used for predicting a genotype’s allelic state at a specific locus/QTL/gene. This is accomplished by using both a genotype matrix and a separate file which has categorizations about loci/QTL/genes of interest for the individuals in the genotypic matrix. A training population can be created from a panel of individuals who have been previously screened for specific loci/QTL/genes, and this previous screening could be summarized into a category. Using the categorization of individuals which have been genotyped using a genome wide marker platform, a model can be trained to predict what category (haplotype) an individual belongs in based on their genetic sequence in the region associated with the locus/QTL/gene. These trained models can then be used to predict the haplotype of a locus/QTL/gene for individuals which have been genotyped with a genome wide platform yet not genotyped for the specific locus/QTL/gene. This package is based off work done by Winn et al 2021. For more specific information on this method, refer to <doi:10.1007/s00122-022-04178-w>.

Zachary Winn

HaploCatcher

A Predictive Haplotyping Package

plot_locus_perm_cv function

<dl><dt>results</dt>
<dd>An object of class "list" which is derived from the "locus_perm_cv" function.</dd>
<dt>individual_images</dt>
<dd>A logical argument that defines if the user wants both the composite image and the full image. Default setting is FALSE.</dd></dl>

Arguments

Visualize Permutation CV Results — plot_locus_perm_cv

<dl>

<dt>results</dt>
<dd>An object of class "list" which is derived from the "locus_perm_cv" function.</dd>


<dt>individual_images</dt>
<dd>A logical argument that defines if the user wants both the composite image and the full image. Default setting is FALSE.</dd>

</dl>

plot_locus_perm_cv: Visualize Permutation CV Results

Description

Usage

Value

Arguments

Examples