summary_to_fitpoly

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.

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

summary_to_fitpoly function

<dl><dt>R_all</dt>
<dd>A data frame containing total signal intensity (R) values. The first
column should be `MarkerName`, and subsequent columns should represent samples.</dd>
<dt>theta_all</dt>
<dd>A data frame containing allelic ratio (theta) values. The first
column should be `MarkerName`, and subsequent columns should represent samples.</dd></dl>

Arguments

Convert Summary Data to FitPoly-Compatible Format — summary_to_fitpoly

<dl>

<dt>R_all</dt>
<dd>A data frame containing total signal intensity (R) values. The first
column should be `MarkerName`, and subsequent columns should represent samples.</dd>


<dt>theta_all</dt>
<dd>A data frame containing allelic ratio (theta) values. The first
column should be `MarkerName`, and subsequent columns should represent samples.</dd>

</dl>

summary_to_fitpoly: Convert Summary Data to FitPoly-Compatible Format

Description

Usage

Value

Arguments

Details