qploidy_read_vcf: Convert VCF File to Qploidy Data

In Qploidy: Estimation of Ploidy and Detection of Aneuploidy Using Genotyping Data

Convert VCF File to Qploidy Data

Description

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.

Usage

qploidy_read_vcf(vcf_file, geno = FALSE, geno.pos = FALSE)

Arguments

vcf_file	Path to the VCF file.
geno	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.
geno.pos	Logical. If TRUE, the output will include MarkerName, Chromosome, and Position columns.

Value

A data frame containing the processed VCF data.

Qploidy documentation built on June 8, 2025, 10 a.m.