test_profile_2 {seqCAT} | R Documentation

## SNV profile 2

### Description

SNV profile in GRanges format from "sample2", originating from the test_profile_2.txt in the inst/extdata directory, for use in unit tests.

### Usage

    data(test_profile_2)

### Format

A GRanges object with 382 elements and 17 metadata columns:

rsID

  mutation ID, if available

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

DP

  total variant depth

AD1

  allelic depth, allele 1

AD2

  allelic depth, allele 2

A1

  allele 1

A2

  allele 2

warnings

  warnings from variant calling

sample

  sample name

[Package seqCAT version 1.6.3 Index]