SampleCoverage: The SampleCoverage class

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

Description

An S4 class containing the genomic location and allele information per sample for each variant from a VCF file.

Slots

Table

A data frame containing the genomic location and allele information per sample for each 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

For each well samples

NR_sampleID

The total numbe rof reads covering the variant location at this smaple

NV_sampleID

Number of reads supporting the variant sequence at this smaple

AF_sampleID

Variant Reads allele fraction at this sample

GT

colon separated list of unphased genotype at each sample

See Also

VariantAlleleInfo, getVariantAlleleInfo, getVariantCoverageTable, plot.VariantAlleleInfo

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