summary_to_fitpoly: Convert Summary Data to FitPoly-Compatible Format

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

Convert Summary Data to FitPoly-Compatible Format

Description

This function processes R (total signal intensity) and theta (allelic ratio) values to generate a data frame compatible with the FitPoly tool. It calculates X and Y values (reference and alternative allele intensities, respectively) and combines them with R and theta into a long-format data frame.

Usage

summary_to_fitpoly(R_all, theta_all)

Arguments

R_all	A data frame containing total signal intensity (R) values. The first column should be 'MarkerName', and subsequent columns should represent samples.
theta_all	A data frame containing allelic ratio (theta) values. The first column should be 'MarkerName', and subsequent columns should represent samples.

Details

The function calculates X and Y values as follows: - 'X = R * (1 - theta)' - 'Y = R * theta' The resulting data frame is in a long format, where each row corresponds to a specific marker-sample combination.

Value

A data frame in long format with the following columns: - 'MarkerName': Marker identifiers. - 'SampleName': Sample identifiers. - 'X': Reference allele intensity. - 'Y': Alternative allele intensity. - 'R': Total signal intensity. - 'ratio': Allelic ratio (theta).

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