vcfR

vcfR provides R functions to manipulate and analyze Variant Call Format (VCF) data and infer copy number variation (CNV) by leveraging allele frequencies at heterozygous positions.

Key Features:

• CNV inference from allele frequencies: Summarizes allele frequencies at heterozygous positions to detect copy number variation.
• Windowed summarization and binning: Aggregates heterozygous positions within arbitrarily sized windows and bins allele frequencies, identifying the bin with highest abundance as a non-parametric summary.
• Ploidy inference: Infers ploidy directly from the data without assuming a base ploidy.
• Support for chromosomes and contigs: Applicable to reference genomes composed of full chromosomes or sub-chromosomal contigs.
• VCF input/output and parsing: Provides functions to read and write VCF files and to parse VCF data into matrices.
• Modular analysis and quality control: Extracted matrices support quality control and modular, flexible downstream analyses for investigating CNV.

Scientific Applications:

• Validation in Saccharomyces cerevisiae: Methodology validated on S. cerevisiae, a model organism with variable copy number.
• Application to Phytophthora infestans: Applied to the oomycete Phytophthora infestans to study CNV.
• Cross-species CNV investigation: Supports genomic projects requiring detailed CNV analysis across diverse species.

Methodology:

Reads and writes VCF files; parses VCF into matrices; summarizes allele frequencies at heterozygous positions within arbitrarily sized windows; bins allele frequencies and identifies the most abundant bin to produce a non-parametric summary; infers ploidy from the data; uses extracted matrices for quality control and downstream analysis.