AnnotateVCFObj: AnnotateVCFObj

In cgab-ncc/FIREVAT: FIREVAT, FInding REliable Variants without ArTifacts

AnnotateVCFObj

Description

Annotates a vcf.obj using df.variants.of.interest (from PrepareAnnotationDB)

Usage

AnnotateVCFObj(
  vcf.obj,
  df.annotation.db,
  columns.to.include,
  include.all.columns = FALSE
)

Arguments

vcf.obj	ReadVCF
df.annotation.db	A data.frame from PrepareAnnotationDB. This data.frame must have the columns 'CHROM', 'POS', 'REF', 'ALT'
columns.to.include	A character vector of columns to include. Note that existing columns in vcf.obj will not be affected.
include.all.columns	A boolean value. If TRUE, then annotates vcf.obj with all columns present in df.variants.of.interest. If FALSE, columns.to.include must be supplied.

Value

An annotated vcf.obj

cgab-ncc/FIREVAT documentation built on Nov. 19, 2022, 5:55 p.m.