simulate_axiom_summary

This function generates a simulated Axiom array summary file with probe IDs ending in `-A` or `-B` and sample intensities. The intensities are simulated based on the genotype of the sample: homozygous for A, homozygous for B, or heterozygous.

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_axiom_summary function

<dl><dt>file_path</dt>
<dd>The path where the simulated summary file will be saved.</dd>
<dt>n_probes</dt>
<dd>Number of probes to simulate. Default is 100.</dd>
<dt>n_samples</dt>
<dd>Number of samples to simulate. Default is 10.</dd>
<dt>seed</dt>
<dd>The seed for random number generation to ensure reproducibility.</dd></dl>

Arguments

Simulate an Axiom array summary file — simulate_axiom_summary

<dl>

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


<dt>n_probes</dt>
<dd>Number of probes to simulate. Default is 100.</dd>


<dt>n_samples</dt>
<dd>Number of samples to simulate. Default is 10.</dd>


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

</dl>

simulate_axiom_summary: Simulate an Axiom array summary file

Description

Usage

Value

Arguments