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 |