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Qploidy (version 1.0.1)

Estimation of Ploidy and Detection of Aneuploidy Using Genotyping Data

Description

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) for higher ploidy levels. Computes B-allele frequencies (BAF), z-scores, and identifies copy number variation patterns.

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Install

install.packages('Qploidy')

Monthly Downloads

167

Version

1.0.1

License

AGPL (>= 3)

Issues

Pull Requests

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Repository

https://github.com/Cristianetaniguti/Qploidy

Maintainer

Cristiane Taniguti

Last Published

May 1st, 2025

Functions in Qploidy (1.0.1)

Calculate the Statistical Mode

plot_qploidy_standardization

Plot Method for Qploidy Standardization

Plot BAF Histogram

Pascal Triangle for Expected Peaks Calculation

qploidy_read_vcf

Convert VCF File to Qploidy Data

summary_to_fitpoly

Convert Summary Data to FitPoly-Compatible Format

Estimate Centers for Standardization Using Updog Bias

Standardize Allelic Ratio Data and Compute BAF and Z-Scores

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

vcf_sanity_check

Perform a Sanity Check on a VCF File

simulate_axiom_summary

Simulate an Axiom array summary file

Convert Axiom Array Summary File to Qploidy Input

Identify and Remove Outliers Based on Bonferroni-Holm Adjusted P-values

read_illumina_array

Read Illumina Array Files

read_qploidy_standardization

Read Qploidy Standardization File

simulate_illumina_file

Simulate an Illumina File

simulate_standardization_input

Simulate Genotyping Data with Flexible Ploidy

Calculate B-Allele Frequency (BAF) from Theta Values

Calculate Z-Scores for Allele Intensities or Counts

indexes for aneuploids

Get R and Theta Values from Summary File

Estimate Cluster Centers for Genotype Dosage Classes

merge_arms_format

Merges chromosome-arm level analysis results into chromosome level format

find_header_line

Find the Header Line in a File

To create baf in parallel

all_resolutions_plots

Plot graphics for ploidy visual inspection for each resolution

Clean Axiom Summary File

area_estimate_ploidy

Estimate ploidy using area method

print.qploidy_area_ploidy_estimation

print qploidy_area_ploidy_estimation object

print.qploidy_standardization

Print method for object of class 'qploidy_standardization'