annotate_variants: Annotate variants and drivers.

In caravagnalab/CNAqc: CNAqc - Copy Number Analysis quality check

Annotate variants and drivers.

Description

Easy and fast way to annotate input mutations, and detect potential driver mutations. This function computes the locations of the different mutations and the consequences of substituions mapped to coding regions, using VariantAnnotation and other Bioconductor packages. Then, putative drivers are annotated upon matching from an input list that, by default, is compiled from the Intogen database. Drivers are selected among coding substituions with known effect.

Usage

annotate_variants(x, drivers = CNAqc::intogen_drivers)

Arguments

x	A CNAqc object.
drivers	A dataframe in the format of the 'intogen_drivers' one released with CNAqc. In particular, it must contain a column named 'gene' to identify gene names.

Value

A CNAqc object with variants annotated. For each variant this object contains:

- 'location' reporting the position of the variant in the genome ('coding', 'intron', 'threeUTR', ...), - 'consequence' with the consequence of coding mutations ('synonymous', 'nonsynonymous', ...), - 'is_driver' a boolean that indicates if the gene is a driver, - 'gene_symbol' for the annotated corresponding gene symbol (if the variant is in a gene) - 'driver_label' with the driver label written as 'gene_refAA->varAA' ('NA' in case 'is_driver = FALSE').

The annotation process is based on the package VariantAnnotation.

Examples

## Not run: 
library(CNAqc)

data('example_dataset_CNAqc', package = 'CNAqc')

mutations <- example_dataset_CNAqc$mutations

mutations_annotated <- annotate_variants(mutations)

## End(Not run)

caravagnalab/CNAqc documentation built on Oct. 31, 2024, 3:54 a.m.