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_R_theta             Get R and Theta Values from Summary 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_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
