annotate_variants: Annotate variants from a vector of variant IDs

In MCorentin/vargen: Fetching Variants Related to Phenotypes Using Public Databases

Annotate variants from a vector of variant IDs

Description

use getVariants and process the output to return a data.frame instead of nested lists.

Usage

annotate_variants(rsid, verbose = FALSE)

Arguments

rsid	a vector of variant IDs
verbose	if TRUE will print progress messages (default = FALSE)

Value

a data.frame with the following columns:

• rsid (variant id)

• cadd phred (phred score from CADD, higher more deleterious)

• fathmm_xf_score (from 0 to 1, higher is more deleterious)

• fathmm_xf_pred ("D"(DAMAGING) if score > 0.5, "N"(NEUTRAL) otherwise)

• annot_type (the annotation type from CADD, eg: "Intergenic")

• consequence (the consequence from CADD, eg: "DOWNSTREAM")

• clinical_significance (risk factor from clinvar, eg: "Benign", "risk factor")

• snpeff_ann (impact annotation from snpeff eg: "MODIFIER")

Examples

annotate_variants(rsid = c("rs1225680362", "rs12395043", "rs746318172"))

MCorentin/vargen documentation built on Feb. 6, 2024, 2:32 p.m.