read_axiom

This function processes an Axiom array summary file and converts it into a 
format compatible with Qploidy and fitpoly analysis.

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

read_axiom function

<dl><dt>summary_file</dt>
<dd>Path to the Axiom summary file.</dd>
<dt>ind_names</dt>
<dd>Optional. A file with two columns: Plate_name (sample IDs 
in the summary file) and Sample_Name (desired sample names).</dd>
<dt>atan</dt>
<dd>Logical. If TRUE, calculates theta using atan2.</dd></dl>

Arguments

Convert Axiom Array Summary File to Qploidy Input — read_axiom

<dl>

<dt>summary_file</dt>
<dd>Path to the Axiom summary file.</dd>


<dt>ind_names</dt>
<dd>Optional. A file with two columns: Plate_name (sample IDs 
in the summary file) and Sample_Name (desired sample names).</dd>


<dt>atan</dt>
<dd>Logical. If TRUE, calculates theta using atan2.</dd>

</dl>

read_axiom: Convert Axiom Array Summary File to Qploidy Input

Description

Usage

Value

Arguments