test_profile_2: SNV profile 2

Description Usage Format

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

1

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


seqCAT documentation built on May 30, 2018, 6 p.m.