Estimation of Ploidy and Detection of Aneuploidy Using Genotyping Data

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Documentation for package ‘Qploidy’ version 1.0.1

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
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_qploidy_standardization Plot Method for Qploidy Standardization
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 Qploidy Standardization File
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