check_replicates

This function checks the compatibility between sample genotypes in a VCF file by comparing all pairs of samples.

Functions developed within Breeding Insight to analyze
diploid and polyploid breeding and genetic data. 'BIGr' provides the
ability to filter variant call format (VCF) files, extract single nucleotide polymorphisms (SNPs)
from diversity arrays technology missing allele discovery count (DArT MADC) files,
and manipulate genotype data for both diploid and polyploid species. It
also serves as the core dependency for the 'BIGapp' 'Shiny' app, which
provides a user-friendly interface for performing routine genotype
analysis tasks such as dosage calling, filtering, principal component analysis (PCA),
genome-wide association studies (GWAS), and
genomic prediction. For more details about the included 'breedTools'
functions, see Funkhouser et al. (2017) <doi:10.2527/tas2016.0003>, and
the 'updog' output format, see Gerard et al. (2018) <doi:10.1534/genetics.118.301468>.

Alexander M. Sandercock

BIGr

Breeding Insight Genomics Functions for Polyploid and Diploid
Species

Cristiane Taniguti

Josue Chinchilla-Vargas

Shufen Chen

Manoj Sapkota

Meng Lin

Dongyan Zhao

Cornell University

check_replicates function

<dl><dt>path.vcf</dt>
<dd>A string specifying the path to the VCF file containing genotype data.</dd>
<dt>select_samples</dt>
<dd>An optional character vector of sample names to be selected for comparison. If NULL (default), all samples in the VCF file are used.</dd>
<dt>verbose</dt>
<dd>A logical value indicating whether to print the number of combinations tested. Default is TRUE.</dd></dl>

Arguments

Compatibility Between Samples Genotypes — check_replicates

<dl>

<dt>path.vcf</dt>
<dd>A string specifying the path to the VCF file containing genotype data.</dd>


<dt>select_samples</dt>
<dd>An optional character vector of sample names to be selected for comparison. If NULL (default), all samples in the VCF file are used.</dd>


<dt>verbose</dt>
<dd>A logical value indicating whether to print the number of combinations tested. Default is TRUE.</dd>

</dl>

check_replicates: Compatibility Between Samples Genotypes

Description

Usage

Value

Arguments

Details

Examples