VariantAlleleInfo: The VariantAlleleInfo class

In chedonat/DigitalPicoTools: DIGITAL ANALYSIS OF PICOGRAM QUANTITIES OF DNA

Description

An S4 class containing the allele information for each variant from a VCF file.

Slots

Table

A data frame containing the Allele information per variant. It gives for each called variants the following information :

Chrom

The chromosome of the variant)

Pos

The position of the variant

REF

The reference sequence

ALT

The altered sequence

Qual

The quality of the variant call

Filter

The VCF filter of the variant call

TC

The total reads count supporting the variant

TR

The total reads count supporting the variant

AF

The reads allele fraction

WR

The total well count at the position of the variant

WV

The count of well supporting the variant

Well_Number

The wells allele fraction

Note

This class is one of the main class of the package

See Also

SampleCoverage, VariantAlleleInfo, getVariantAlleleInfo, getVariantCoverageTable, plot.VariantAlleleInfo

chedonat/DigitalPicoTools documentation built on May 13, 2019, 3:39 p.m.