simulate_vcf

Simulate a VCF file with GT, DP, and AD format fields for 2 chromosomes

Provides functions for estimating ploidy levels and detecting aneuploidy in individuals using
allele intensities or allele count data from high-throughput genotyping platforms, including
single nucleotide polymorphism (SNP) arrays and sequencing-based technologies. Implements an extended version of the 'PennCNV'
signal standardization method by Wang et al. (2007) <doi:10.1101/gr.6861907> for higher ploidy
levels. Computes B-allele frequencies (BAF), z-scores, and identifies copy number variation patterns.

Cristiane Taniguti

Qploidy

Estimation of Ploidy and Detection of Aneuploidy Using
Genotyping Data

Jeekin Lau

David Byrne

Oscar Riera-Lizarazu

simulate_vcf function

<dl><dt>file_path</dt>
<dd>The path where the simulated VCF file will be saved.</dd>
<dt>seed</dt>
<dd>The seed for random number generation to ensure reproducibility.</dd>
<dt>n_tetraploid</dt>
<dd>Number of tetraploid samples. Default is 35.</dd>
<dt>n_diploid</dt>
<dd>Number of diploid samples. Default is 5.</dd>
<dt>n_triploid</dt>
<dd>Number of triploid samples. Default is 10.</dd>
<dt>n_markers</dt>
<dd>Number of markers to simulate. Default is 100.</dd></dl>

Arguments

Simulate a VCF file with GT, DP, and AD format fields for 2 chromosomes — simulate_vcf

<dl>

<dt>file_path</dt>
<dd>The path where the simulated VCF file will be saved.</dd>


<dt>seed</dt>
<dd>The seed for random number generation to ensure reproducibility.</dd>


<dt>n_tetraploid</dt>
<dd>Number of tetraploid samples. Default is 35.</dd>


<dt>n_diploid</dt>
<dd>Number of diploid samples. Default is 5.</dd>


<dt>n_triploid</dt>
<dd>Number of triploid samples. Default is 10.</dd>


<dt>n_markers</dt>
<dd>Number of markers to simulate. Default is 100.</dd>

</dl>

simulate_vcf: Simulate a VCF file with GT, DP, and AD format fields for 2 chromosomes

Description

Usage

Value

Arguments