query_vcf: Query VCF Data

In AndersenLab/cegwas2: C. elegans genome-wide association

Description

query_vcf enables you to query variants within a VCF

Usage

query_vcf(..., info = c(), format = c("TGT"), impact = c("MODERATE",
  "HIGH"), samples = "ALL", long = TRUE, vcf = get_vcf())

Arguments

...	Gene names, regions, or wormbase identifiers to query.
info	Info columns to output. If an ANN (annotation) column is available it is automatically fetched. [Default c()]
format	Format columns to output. A "GT" or "TGT" column must be specified to retrieve genotypes. GT: uses a numeric represetnation (0=REF, 1=ALT) and outputs g1, g2, and genotype (0=REF homozygous, 1=HET, 2=ALT homozygous). TGT: uses the base representation (ATGC) and outputs two columns: a1, a2.
impact	A vector of impact levels to filter on (LOW, MODERATE, HIGH, MODIFIER). "ALL" can be used to return ALL variants. [Default c('MODERATE', 'HIGH')]
samples	A set of samples to subset on [default: "ALL"]
long	Return dataset in long or wide format. [Default TRUE]
vcf	Use a custom VCF.

Value

Dataframe with variant data

Examples

query_vcf("pot-2","II:1-10000","WBGene00010785")

AndersenLab/cegwas2 documentation built on Aug. 26, 2020, 4:43 p.m.