gene_comp

A data frame which contains information from 1345 unique wheat lines on the Sst1 solid stem locus.

datasets

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

gene_comp function

A data frame with 1345 rows and 7 columns:
<dl><dt>Trait</dt>
<dd>A short discription of the phenotype associated with the gene</dd><dt>Chromosome</dt>
<dd>The chromosome where the gene resides</dd><dt>Gene</dt>
<dd>The name of the gene</dd><dt>Nursery</dt>
<dd>The program which produced the gene call for the genotype</dd><dt>Line</dt>
<dd>A breeder assigned line designation</dd><dt>FullSampleName</dt>
<dd>A designation unique to the line found in the genotypic matrix</dd><dt>Call</dt>
<dd>A 'call' given for the allelic state. For this package, it is best to format the non desiarable allele as "non_gene" and the heterozygous state as "het_gene".</dd></dl>

Format

Model Gene Compendium Data Set — gene_comp

A data frame with 1345 rows and 7 columns:
<dl>

<dt>Trait</dt>
<dd>A short discription of the phenotype associated with the gene</dd>

<dt>Chromosome</dt>
<dd>The chromosome where the gene resides</dd>

<dt>Gene</dt>
<dd>The name of the gene</dd>

<dt>Nursery</dt>
<dd>The program which produced the gene call for the genotype</dd>

<dt>Line</dt>
<dd>A breeder assigned line designation</dd>

<dt>FullSampleName</dt>
<dd>A designation unique to the line found in the genotypic matrix</dd>

<dt>Call</dt>
<dd>A 'call' given for the allelic state. For this package, it is best to format the non desiarable allele as "non_gene" and the heterozygous state as "het_gene".</dd>



</dl>

gene_comp: Model Gene Compendium Data Set

Description

Usage

Arguments

Format

Examples