qploidy_read_vcf

This function converts a VCF file into a format compatible with Qploidy 
analysis. It extracts genotype and allele depth information and formats 
it into a data frame.

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

qploidy_read_vcf function

<dl><dt>vcf_file</dt>
<dd>Path to the VCF file.</dd>
<dt>geno</dt>
<dd>Logical. If TRUE, the output columns will include MarkerName, 
SampleName, geno, and prob. If FALSE, the output will include MarkerName, 
SampleName, X, Y, R, and ratio.</dd>
<dt>geno.pos</dt>
<dd>Logical. If TRUE, the output will include MarkerName, 
Chromosome, and Position columns.</dd></dl>

Arguments

Convert VCF File to Qploidy Data — qploidy_read_vcf

<dl>

<dt>vcf_file</dt>
<dd>Path to the VCF file.</dd>


<dt>geno</dt>
<dd>Logical. If TRUE, the output columns will include MarkerName, 
SampleName, geno, and prob. If FALSE, the output will include MarkerName, 
SampleName, X, Y, R, and ratio.</dd>


<dt>geno.pos</dt>
<dd>Logical. If TRUE, the output will include MarkerName, 
Chromosome, and Position columns.</dd>

</dl>

qploidy_read_vcf: Convert VCF File to Qploidy Data

Description

Usage

Value

Arguments