test_comparison {seqCAT} | R Documentation

## Overlapping and compared SNVs

### Description

Overlapping and compared variants from "sample1" and "sample2" originating from the example.vcf file included in the inst/extdata directory, for use in unit tests.

### Usage

    data(test_comparison)

### Format

A dataframe with 51 rows and 39 columns:

chr

  chromosome

pos

  SNV position

DP.sample_1

  total variant depth, sample 1

AD1.sample_1

  allelic depth, allele 1, sample 1

AD2.sample_1

  allelic depth, allele 2, sample 1

A1.sample_1

  allele 1, sample 1

A2.sample_1

  allele 2, sample 1

warnings.sample_1

  warnings from variant calling, sample 1

DP.sample_2

  total variant depth, sample 2

AD1.sample_2

  allelic depth, allele 1, sample 2

AD2.sample_2

  allelic depth, allele 2, sample 2

A1.sample_2

  allele 1, sample 2

A2.sample_2

  allele 2, sample 2

warnings.sample_2

  warnings from variant calling, sample 2

sample_1

  name, sample 1

sample_2

  name, sample 2

match

  status of genotype comparison

rsID

  mutation ID

gene

  associated gene

ENSGID

  ensembl gene ID

ENSTID

  ensembl transcript ID

REF

  reference allele

ALT

  alternative allele

impact

  putative variant impact

effect

  variant effect

feature

  transcript feature

biotype

  transcript biotype

[Package seqCAT version 1.8.1 Index]