Man pages for Qploidy
Estimation of Ploidy and Detection of Aneuploidy Using Genotyping Data
| all_resolutions_plots | Plot graphics for ploidy visual inspection for each... |
| 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... |
| 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... |
| plot_qploidy_standardization | Plot Method for Qploidy Standardization |
| plot_xy_with_ploidy_guides | Plot X–Y scatter with ploidy dosage guide lines and optional... |
| 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... |
| rm_outlier | Identify and Remove Outliers Based on Bonferroni-Holm... |
| 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... |
| 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 |
