Estimation of Ploidy and Detection of Aneuploidy Using Genotyping Data
Plot graphics for ploidy visual inspection for each resolution
Estimate ploidy using area method
Clean Axiom Summary File
Find the Header Line in a File
indexes for aneuploids
To create baf in parallel
Calculate B-Allele Frequency (BAF) from Theta Values
Estimate Cluster Centers for Genotype Dosage Classes
Get R and Theta Values from Summary File
Calculate Z-Scores for Allele Intensities or Counts
Merges chromosome-arm level analysis results into chromosome level for...
Calculate the Statistical Mode
Pascal Triangle for Expected Peaks Calculation
Plot BAF Histogram
Plot BAF
Plot Method for Qploidy Standardization
print qploidy_area_ploidy_estimation object
Print method for object of class 'qploidy_standardization'
Convert VCF File to Qploidy Data
Convert Axiom Array Summary File to Qploidy Input
Read Illumina Array Files
Read Qploidy Standardization File
Identify and Remove Outliers Based on Bonferroni-Holm Adjusted P-value...
Simulate an Axiom array summary file
Simulate an Illumina File
Simulate Genotyping Data with Flexible Ploidy
Simulate a VCF file with GT, DP, and AD format fields for 2 chromosome...
Standardize Allelic Ratio Data and Compute BAF and Z-Scores
Convert Summary Data to FitPoly-Compatible Format
Estimate Centers for Standardization Using Updog Bias
Perform a Sanity Check on a VCF File
Provides functions for estimating ploidy levels and detecting aneuploidy in individuals using allele intensities or allele count data from high-throughput genotyping platforms, including single nucleotide polymorphism (SNP) arrays and sequencing-based technologies. Implements an extended version of the 'PennCNV' signal standardization method by Wang et al. (2007) <doi:10.1101/gr.6861907> for higher ploidy levels. Computes B-allele frequencies (BAF), z-scores, and identifies copy number variation patterns.
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