# Estimation of Ploidy and Detection of Aneuploidy Using Genotyping Data

## Documentation for package ‘Qploidy’ version 1.5.4

- DESCRIPTION file.
- User guides, package vignettes and other documentation.
- Package NEWS.

## Help Pages

all_resolutions_plots | Plot graphics for ploidy visual inspection for each resolution
area_estimate_ploidy | Estimate ploidy using area method
clean_summary | Clean Axiom Summary File
find_header_line | Find the Header Line in a File
get_aneuploids | indexes for aneuploids
get_baf | Calculate B-Allele Frequency (BAF) from Theta Values
get_baf_par | To create baf in parallel
get_centers | Estimate Cluster Centers for Genotype Dosage Classes
get_R_theta | Get R and Theta Values from Summary File
get_zscore | Calculate Z-Scores for Allele Intensities or Counts
is_compressed_file | Check if a File is Compressed
merge_arms_format | Merges chromosome-arm level analysis results into chromosome level format
mode | Calculate the Statistical Mode
pascalTriangle | Pascal Triangle for Expected Peaks Calculation
plot_baf | Plot BAF
plot_baf_hist | Plot BAF Histogram
plot_baf_with_ploidy_guides | Plot BAF-derived X–Y scatter with ploidy dosage guides (optional sample highlighting)
plot_qploidy_standardization | Plot Method for Qploidy Standardization
plot_xy_with_ploidy_guides | Plot X–Y scatter with ploidy dosage guide lines and optional sample highlighting
print.qploidy_area_ploidy_estimation | print qploidy_area_ploidy_estimation object
print.qploidy_standardization | Print method for object of class 'qploidy_standardization'
qploidy_read_vcf | Convert VCF File to Qploidy Data
read_axiom | Convert Axiom Array Summary File to Qploidy Input
read_illumina_array | Read Illumina Array Files
read_qploidy_standardization | Read a Qploidy Standardized Dataset (.tsv or .tsv.gz) with format checks
rm_outlier | Identify and Remove Outliers Based on Bonferroni-Holm Adjusted P-values
simulate_axiom_summary | Simulate an Axiom array summary file
simulate_illumina_file | Simulate an Illumina File
simulate_standardization_input | Simulate Genotyping Data with Flexible Ploidy
simulate_vcf | Simulate a VCF file with GT, DP, and AD format fields for 2 chromosomes
standardize | Standardize Allelic Ratio Data and Compute BAF and Z-Scores
summary_to_fitpoly | Convert Summary Data to FitPoly-Compatible Format
updog_centers | Estimate Centers for Standardization Using Updog Bias
vcf_sanity_check | Perform a Sanity Check on a VCF File
write_qploidy_standardization | Write Qploidy Standardization Object to File