read_axiom: Convert Axiom Array Summary File to Qploidy Input

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

Convert Axiom Array Summary File to Qploidy Input

Description

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

Usage

read_axiom(summary_file, ind_names = NULL, atan = FALSE)

Arguments

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

Value

A data frame formatted for Qploidy analysis, containing the following columns: - 'MarkerName': Marker identifiers. - 'SampleName': Sample identifiers (if 'ind_names' is provided, these will be updated accordingly). - 'X': Reference allele intensity (calculated if applicable). - 'Y': Alternative allele intensity (calculated if applicable). - 'R': Total signal intensity (calculated if applicable). - 'ratio': Allelic ratio (theta, calculated if applicable). - Additional columns may be included depending on the input data and processing steps.

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