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Table 1 A complete description of package functionality and executable examples can be found in the vignette and manual of VPA

From: VPA: an R tool for analyzing sequencing variants with user-specified frequency pattern

Function Description
LoadFiltering Load data from study subjects and perform position-level quality filtering
Patterning Prioritize sequencing variants in user-specified frequency pattern
read.vcf Read data file in VCF format
write.vcf Write a VCF format object to a file
filtervcf Filter sequencing variants with user-specified quality criteria
filterpos Filter sequencing variants against known SNP datasets
Pos2Gene Annotate sequencing variants into genes
gefreq Frequency analysis at the gene level (for aggregates of variants)
subvcf Extract a subset of variants from a VCF format object
pos2seq Retrieve information for position of interest from tabix indexed data file
vcfreq Summarize the frequencies of sequencing variants