---
title: "Qploidy_res"
output: html_document
---

# Qploidy Results Overview

This document summarizes the main types of results users can obtain from the Qploidy package:

## Ploidy CSV File
A table of estimated ploidy levels for each sample and chromosome, typically generated after running the HMM-based copy number estimation. Includes columns for sample name, chromosome, estimated ploidy, and confidence metrics.

## Qploidy Data
Standardized SNP-level data for all samples and chromosomes, including normalized allele counts or intensities, B-allele frequency (BAF), and z-scores. This data is used for downstream analyses and visualization.

## Copy Number (CN) Calls
Windowed copy number calls per sample and chromosome, as produced by `hmm_estimate_CN` or `hmm_estimate_CN_multi`. Includes CN state, posterior probabilities, and window summary statistics.

## Visualization Plots
Plots of BAF, z-score, and copy number tracks for each sample and chromosome, including guides for expected ploidy states. Useful for visual inspection and reporting.

## Standardization Reports
Summary metrics and diagnostic plots from the standardization process, including outlier detection and normalization quality checks.

## Input/Output Format Examples
Help files and vignettes provide example input formats (VCF, array, CSV/TSV, fitpoly) and example output tables for easy reference.

## Shiny App Outputs
Interactive results and downloadable tables from the Qploidy Shiny app, including ploidy tables, CN tracks, and visualizations.

For more details and code examples, see the Qploidy vignette and help files included in the package.
